{"$update": {"2659": {"$update": {"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": {"$insert": {"35954": {"category_aro_name": "ciprofloxacin", "category_aro_cvterm_id": "35954", "category_aro_accession": "0000036", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome."}}}}}, "1146": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. 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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."}, "35932": {"category_aro_name": "amikacin", "category_aro_cvterm_id": "35932", "category_aro_accession": "0000013", "category_aro_class_name": "Antibiotic", "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."}, "46133": {"category_aro_name": "gentamicin", "category_aro_cvterm_id": "46133", "category_aro_accession": "3007382", "category_aro_class_name": "Antibiotic", "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)."}, "35924": {"category_aro_name": "neomycin", "category_aro_cvterm_id": "35924", "category_aro_accession": "0000005", "category_aro_class_name": "Antibiotic", "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."}, "35969": {"category_aro_name": "tobramycin", "category_aro_cvterm_id": "35969", "category_aro_accession": "0000052", "category_aro_class_name": "Antibiotic", "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."}}}}}, "662": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. 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They are mostly used for agriculture and veterinary purposes."}, "37015": {"category_aro_name": "tiamulin", "category_aro_cvterm_id": "37015", "category_aro_accession": "3000671", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation."}}}}}, "5917": {"$update": {"ARO_category": {"$insert": {"36284": {"category_aro_name": "tylosin", "category_aro_cvterm_id": "36284", "category_aro_accession": "3000145", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis."}, "36297": {"category_aro_name": "azithromycin", "category_aro_cvterm_id": "36297", "category_aro_accession": "3000158", "category_aro_class_name": "Antibiotic", "category_aro_description": "Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation."}, "35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "category_aro_description": "Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited."}}}}}, "5916": {"$update": {"ARO_category": {"$insert": {"35964": {"category_aro_name": "lincomycin", "category_aro_cvterm_id": "35964", "category_aro_accession": "0000046", "category_aro_class_name": "Antibiotic", "category_aro_description": "Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction."}, "35983": {"category_aro_name": "clindamycin", "category_aro_cvterm_id": "35983", "category_aro_accession": "0000066", "category_aro_class_name": "Antibiotic", "category_aro_description": "Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria."}}}}}, "1380": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2794": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"$insert": {"13112": "A2142G"}}, "clinical": {"$insert": {"13112": "A2142G"}}}}}}}}, "3825": {"$update": {"ARO_category": {"$insert": {"35946": {"category_aro_name": "roxithromycin", "category_aro_cvterm_id": "35946", "category_aro_accession": "0000027", "category_aro_class_name": "Antibiotic", "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."}, "35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "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."}, "35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "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."}}}}}, "3824": {"$update": {"ARO_category": {"$insert": {"35946": {"category_aro_name": "roxithromycin", "category_aro_cvterm_id": "35946", "category_aro_accession": "0000027", "category_aro_class_name": "Antibiotic", "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. 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Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited."}}}}}, "3823": {"$update": {"ARO_category": {"$insert": {"35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "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. 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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."}, "35932": {"category_aro_name": "amikacin", "category_aro_cvterm_id": "35932", "category_aro_accession": "0000013", "category_aro_class_name": "Antibiotic", "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."}, "46133": {"category_aro_name": "gentamicin", "category_aro_cvterm_id": "46133", "category_aro_accession": "3007382", "category_aro_class_name": "Antibiotic", "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)."}, "35924": {"category_aro_name": "neomycin", "category_aro_cvterm_id": "35924", "category_aro_accession": "0000005", "category_aro_class_name": "Antibiotic", "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."}, "35969": {"category_aro_name": "tobramycin", "category_aro_cvterm_id": "35969", "category_aro_accession": "0000052", "category_aro_class_name": "Antibiotic", "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."}}}, "model_param": {"$insert": {"snp": {"param_type": "single resistance variant", "param_value": {"13134": "D89V"}, "clinical": {"13134": "D89V"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}}, "model_type": "protein overexpression model", "model_description": "Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.", "model_type_id": "41091"}}, "193": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "314": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "115": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3993": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "277": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "398": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "86": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "87": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3278": {"$update": {"ARO_category": {"$insert": {"35988": {"category_aro_name": "levofloxacin", "category_aro_cvterm_id": "35988", "category_aro_accession": "0000071", "category_aro_class_name": "Antibiotic", "category_aro_description": "Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication."}, "37005": {"category_aro_name": "nalidixic acid", "category_aro_cvterm_id": "37005", "category_aro_accession": "3000661", "category_aro_class_name": "Antibiotic", "category_aro_description": "Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments."}}}}}, "797": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "647": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "4128": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "836": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2783": {"$insert": {"model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}}}, "378": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "4123": {"$update": {"ARO_category": {"$insert": {"36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "40944": {"category_aro_name": "moxalactam", "category_aro_cvterm_id": "40944", "category_aro_accession": "3004017", "category_aro_class_name": "Antibiotic", "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."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35976": {"category_aro_name": "cefepime", "category_aro_cvterm_id": "35976", "category_aro_accession": "0000059", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "40931": {"category_aro_name": "cefotetan", "category_aro_cvterm_id": "40931", "category_aro_accession": "3004004", "category_aro_class_name": "Antibiotic", "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."}, "42781": {"category_aro_name": "cefpirome", "category_aro_cvterm_id": "42781", "category_aro_accession": "3004726", "category_aro_class_name": "Antibiotic", "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."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "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."}, "46458": {"category_aro_name": "oxacephem", "category_aro_cvterm_id": "46458", "category_aro_accession": "3007676", "category_aro_class_name": "Drug Class", "category_aro_description": "An oxacephem is a beta-lactam molecule similar to a cephem, but with an oxygen substituted for the sulfur. They show marked enhancement in their antibacterial activity."}, "40941": {"category_aro_name": "flomoxef", "category_aro_cvterm_id": "40941", "category_aro_accession": "3004014", "category_aro_class_name": "Antibiotic", "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."}}}}}, "3983": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "4127": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "4126": {"$update": {"ARO_category": {"$insert": {"36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "40944": {"category_aro_name": "moxalactam", "category_aro_cvterm_id": "40944", "category_aro_accession": "3004017", "category_aro_class_name": "Antibiotic", "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."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35976": {"category_aro_name": "cefepime", "category_aro_cvterm_id": "35976", "category_aro_accession": "0000059", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "40931": {"category_aro_name": "cefotetan", "category_aro_cvterm_id": "40931", "category_aro_accession": "3004004", "category_aro_class_name": "Antibiotic", "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."}, "42781": {"category_aro_name": "cefpirome", "category_aro_cvterm_id": "42781", "category_aro_accession": "3004726", "category_aro_class_name": "Antibiotic", "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."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "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."}, "46458": {"category_aro_name": "oxacephem", "category_aro_cvterm_id": "46458", "category_aro_accession": "3007676", "category_aro_class_name": "Drug Class", "category_aro_description": "An oxacephem is a beta-lactam molecule similar to a cephem, but with an oxygen substituted for the sulfur. They show marked enhancement in their antibacterial activity."}, "40941": {"category_aro_name": "flomoxef", "category_aro_cvterm_id": "40941", "category_aro_accession": "3004014", "category_aro_class_name": "Antibiotic", "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."}}}}}, "4125": {"$update": {"ARO_category": {"$insert": {"36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "40944": {"category_aro_name": "moxalactam", "category_aro_cvterm_id": "40944", "category_aro_accession": "3004017", "category_aro_class_name": "Antibiotic", "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."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35976": {"category_aro_name": "cefepime", "category_aro_cvterm_id": "35976", "category_aro_accession": "0000059", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "40931": {"category_aro_name": "cefotetan", "category_aro_cvterm_id": "40931", "category_aro_accession": "3004004", "category_aro_class_name": "Antibiotic", "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."}, "42781": {"category_aro_name": "cefpirome", "category_aro_cvterm_id": "42781", "category_aro_accession": "3004726", "category_aro_class_name": "Antibiotic", "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."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "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."}, "46458": {"category_aro_name": "oxacephem", "category_aro_cvterm_id": "46458", "category_aro_accession": "3007676", "category_aro_class_name": "Drug Class", "category_aro_description": "An oxacephem is a beta-lactam molecule similar to a cephem, but with an oxygen substituted for the sulfur. They show marked enhancement in their antibacterial activity."}, "40941": {"category_aro_name": "flomoxef", "category_aro_cvterm_id": "40941", "category_aro_accession": "3004014", "category_aro_class_name": "Antibiotic", "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."}}}}}, "4124": {"$update": {"ARO_category": {"$insert": {"36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "40944": {"category_aro_name": "moxalactam", "category_aro_cvterm_id": "40944", "category_aro_accession": "3004017", "category_aro_class_name": "Antibiotic", "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."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35976": {"category_aro_name": "cefepime", "category_aro_cvterm_id": "35976", "category_aro_accession": "0000059", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "40931": {"category_aro_name": "cefotetan", "category_aro_cvterm_id": "40931", "category_aro_accession": "3004004", "category_aro_class_name": "Antibiotic", "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."}, "42781": {"category_aro_name": "cefpirome", "category_aro_cvterm_id": "42781", "category_aro_accession": "3004726", "category_aro_class_name": "Antibiotic", "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."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "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."}, "46458": {"category_aro_name": "oxacephem", "category_aro_cvterm_id": "46458", "category_aro_accession": "3007676", "category_aro_class_name": "Drug Class", "category_aro_description": "An oxacephem is a beta-lactam molecule similar to a cephem, but with an oxygen substituted for the sulfur. They show marked enhancement in their antibacterial activity."}, "40941": {"category_aro_name": "flomoxef", "category_aro_cvterm_id": "40941", "category_aro_accession": "3004014", "category_aro_class_name": "Antibiotic", "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."}}}}}, "1525": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2078": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"12951": "A1408G"}, "clinical": {"12951": "A1408G"}}}}}}}, "918": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2661": {"$update": {"ARO_description": "AcrA is a subunit of the AcrAB-TolC multidrug efflux system found in E. coli."}}, "2262": {"$update": {"ARO_description": "mef(C) is a macrolide efflux gene isolated from a plasmid in Photobacterium damselae.", "CARD_short_name": "mef(C)", "ARO_category": {"$insert": {"36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "37012": {"category_aro_name": "oxytetracycline", "category_aro_cvterm_id": "37012", "category_aro_accession": "3000668", "category_aro_class_name": "Antibiotic", "category_aro_description": "Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines."}}}, "model_name": "mef(C)", "ARO_name": "mef(C)"}}, "3982": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1401": {"$update": {"ARO_description": "mef(E) is a proton motive efflux pump in Streptococcus pneumoniae that confers resistance to macrolides. It is found on the same operon as mefA and the ABC-efflux pump mel.", "CARD_short_name": "mef(E)", "ARO_category": {"$insert": {"35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "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."}}}, "model_name": "mef(E)", "ARO_name": "mef(E)"}}, "2070": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"12973": "A1401G"}, "clinical": {"12973": "A1401G"}}}}}}}, "425": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2076": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"12974": "C1198U"}, "clinical": {"12974": "C1198U"}}}}}}}, "1655": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. 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Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1339": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_value": {"$delete": ["9497"], "$insert": {"13020": "C207G"}}}}}}}}, "580": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2122": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"12982": "A1355G"}, "clinical": {"12982": "A1355G"}}}}}}}, "302": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1066": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1137": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "5944": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. 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Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "589": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1667": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "247": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "383": {"$update": {"ARO_category": {"$insert": {"46471": {"category_aro_name": "transmembrane protein conferring colistin resistance", "category_aro_cvterm_id": "46471", "category_aro_accession": "3007684", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin."}}}}}, "406": {"$update": {"ARO_category": {"$insert": {"36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "35980": {"category_aro_name": "cefuroxime", "category_aro_cvterm_id": "35980", "category_aro_accession": "0000063", "category_aro_class_name": "Antibiotic", "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."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}}}}}, "1954": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3784": {"$update": {"ARO_category": {"$insert": {"36220": {"category_aro_name": "glycopeptide antibiotic", "category_aro_cvterm_id": "36220", "category_aro_accession": "3000081", "category_aro_class_name": "Drug Class", "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."}, "35947": {"category_aro_name": "vancomycin", "category_aro_cvterm_id": "35947", "category_aro_accession": "0000028", "category_aro_class_name": "Antibiotic", "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."}}}}, "$insert": {"model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}}}, "102": {"$update": {"ARO_category": {"$update": {"39785": {"$update": {"category_aro_description": "The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, and aztreonam but was susceptible to amikacin, cefotetan, and imipenem."}}}, "$delete": ["35920"]}}}, "1542": {"$update": {"ARO_category": {"$insert": {"35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "category_aro_description": "Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins."}, "36297": {"category_aro_name": "azithromycin", "category_aro_cvterm_id": "36297", "category_aro_accession": "3000158", "category_aro_class_name": "Antibiotic", "category_aro_description": "Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation."}, "35969": {"category_aro_name": "tobramycin", "category_aro_cvterm_id": "35969", "category_aro_accession": "0000052", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}}}}}, "100": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_value": {"$delete": ["9511"], "$insert": {"13005": "A11G"}}}}}}}}, "101": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. 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The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}}}, "808": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. 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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."}, "36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}}}}}, "331": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1320": {"$update": {"ARO_category": {"$insert": {"46471": {"category_aro_name": "transmembrane protein conferring colistin resistance", "category_aro_cvterm_id": "46471", "category_aro_accession": "3007684", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin."}}}}}, "1337": {"$update": {"model_sequences": {"$update": {"sequence": {"8726": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGAATTACCGATTGACGAAAACACGCCACGCATTTTGATTGTGGAAGACGAGCCTAAGCTTGGGCAGTTACTGATCGACTATTTACGTGCGGCCAGCTACGCCCCGTCGCTTATCAGCCATGGCGATCAGGTGTTACCGTACGTGCGCCAGACGCCGCCGGATCTGATCCTGCTGGATTTGATGCTCCCCGGCACGGACGGCCTGACCCTGTGCCGGGAAATTCGTCGCTTCTCCGACGTGCCGATCGTCATGGTGACGGCAAAAATCGAAGAGATCGACCGCCTGCTGGGACTCGAAATTGGCGCGGACGATTACATCTGCAAACCCTACAGCCCGCGTGAAGTGGTCGCCCGCGTGAAAACCATTCTGCGTCGCTGTAAGCCGCAGCGCGAGCTTCAGGTGCTGGACGCCGAAAGCCCGCTGATTGTTGATGAGAGCCGCTTCCAGGCCAGCTGGCGCAGCAAGCTTCTCGATCTCACGCCTGCTGAGTTCCGCCTGCTGAAAACCCTTTCCCACGAGCCGGGGAAAGTGTTCTCTCGCGAGCAGCTGCTCAACCACCTGTATGACGATTACCGCGTGGTGACGGACCGCACCATCGACAGCCACATCAAAAACCTGCGCCGTAAGCTGGAGGCGCTCGACGCCGAACAGTCATTTATTCGCGCGGTGTATGGCGTGGGATACCGCTGGGAAGCGGATGCGTGCAGGATTGCATAG", "fmax": "3480582", "accession": "CP001918.1", "fmin": "3479859", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae subsp. cloacae ATCC 13047", "NCBI_taxonomy_id": "716541", "NCBI_taxonomy_cvterm_id": "37608"}, "protein_sequence": {"accession": "ADF62940.1", "sequence": "MTELPIDENTPRILIVEDEPKLGQLLIDYLRAASYAPSLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDVPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQVLDAESPLIVDESRFQASWRSKLLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLEALDAEQSFIRAVYGVGYRWEADACRIA"}}}}}, "ARO_category": {"$insert": {"35966": {"category_aro_name": "kanamycin A", "category_aro_cvterm_id": "35966", "category_aro_accession": "0000049", "category_aro_class_name": "Antibiotic", "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."}, "35932": {"category_aro_name": "amikacin", "category_aro_cvterm_id": "35932", "category_aro_accession": "0000013", "category_aro_class_name": "Antibiotic", "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."}, "46133": {"category_aro_name": "gentamicin", "category_aro_cvterm_id": "46133", "category_aro_accession": "3007382", "category_aro_class_name": "Antibiotic", "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)."}, "35924": {"category_aro_name": "neomycin", "category_aro_cvterm_id": "35924", "category_aro_accession": "0000005", "category_aro_class_name": "Antibiotic", "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."}, "35969": {"category_aro_name": "tobramycin", "category_aro_cvterm_id": "35969", "category_aro_accession": "0000052", "category_aro_class_name": "Antibiotic", "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."}}}, "model_param": {"$insert": {"snp": {"param_type": "single resistance variant", "param_value": {"13135": "S104N"}, "clinical": {"13135": "S104N"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}}, "model_type": "protein overexpression model", "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_type_id": "41091"}}, "317": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "592": {"$update": {"ARO_category": {"$insert": {"36174": {"category_aro_name": "nucleoside antibiotic", "category_aro_cvterm_id": "36174", "category_aro_accession": "3000034", "category_aro_class_name": "Drug Class", "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."}, "35964": {"category_aro_name": "lincomycin", "category_aro_cvterm_id": "35964", "category_aro_accession": "0000046", "category_aro_class_name": "Antibiotic", "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."}, "35965": {"category_aro_name": "puromycin", "category_aro_cvterm_id": "35965", "category_aro_accession": "0000047", "category_aro_class_name": "Antibiotic", "category_aro_description": "Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation."}}}}}, "1422": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "68": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2907": {"$update": {"ARO_category": {"$insert": {"37713": {"category_aro_name": "retapamulin", "category_aro_cvterm_id": "37713", "category_aro_accession": "3001314", "category_aro_class_name": "Antibiotic", "category_aro_description": "Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections."}, "37013": {"category_aro_name": "virginiamycin M1", "category_aro_cvterm_id": "37013", "category_aro_accession": "3000669", "category_aro_class_name": "Antibiotic", "category_aro_description": "Virginiamycin M1 is a streptogramin A antibiotic."}, "37014": {"category_aro_name": "pleuromutilin antibiotic", "category_aro_cvterm_id": "37014", "category_aro_accession": "3000670", "category_aro_class_name": "Drug Class", "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."}, "37015": {"category_aro_name": "tiamulin", "category_aro_cvterm_id": "37015", "category_aro_accession": "3000671", "category_aro_class_name": "Antibiotic", "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."}, "35952": {"category_aro_name": "streptogramin A antibiotic", "category_aro_cvterm_id": "35952", "category_aro_accession": "0000034", "category_aro_class_name": "Drug Class", "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."}, "36174": {"category_aro_name": "nucleoside antibiotic", "category_aro_cvterm_id": "36174", "category_aro_accession": "3000034", "category_aro_class_name": "Drug Class", "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."}, "46411": {"category_aro_name": "iboxamycin", "category_aro_cvterm_id": "46411", "category_aro_accession": "3007636", "category_aro_class_name": "Antibiotic", "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."}, "46413": {"category_aro_name": "hygromycin A", "category_aro_cvterm_id": "46413", "category_aro_accession": "3007638", "category_aro_class_name": "Antibiotic", "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."}, "46414": {"category_aro_name": "A201A", "category_aro_cvterm_id": "46414", "category_aro_accession": "3007639", "category_aro_class_name": "Antibiotic", "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."}}}}}, "5669": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "5668": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. 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Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "709": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1421": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. 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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."}, "35947": {"category_aro_name": "vancomycin", "category_aro_cvterm_id": "35947", "category_aro_accession": "0000028", "category_aro_class_name": "Antibiotic", "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."}}}}, "$insert": {"model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}}}, "1600": {"$update": {"ARO_category": {"$insert": {"46471": {"category_aro_name": "transmembrane protein conferring colistin resistance", "category_aro_cvterm_id": "46471", "category_aro_accession": "3007684", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin."}}}}}, "2782": {"$insert": {"model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}}}, "2086": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"$delete": ["3071", "2988", "4845"], "$insert": {"12977": "A1055G", "12978": "C1054U", "12979": "G1053A"}}, "clinical": {"$delete": ["3071", "2988", "4845"], "$insert": {"12977": "A1055G", "12978": "C1054U", "12979": "G1053A"}}}}}}}}, "940": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3981": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "472": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2000": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "471": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "476": {"$update": {"ARO_category": {"$insert": {"35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "category_aro_description": "Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins."}, "36297": {"category_aro_name": "azithromycin", "category_aro_cvterm_id": "36297", "category_aro_accession": "3000158", "category_aro_class_name": "Antibiotic", "category_aro_description": "Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation."}, "35969": {"category_aro_name": "tobramycin", "category_aro_cvterm_id": "35969", "category_aro_accession": "0000052", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}}}}}, "3989": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2004": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "2142": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"12985": "G1475U", "12984": "G1475A"}, "clinical": {"12985": "G1475U", "12984": "G1475A"}}}}}}}, "3985": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3986": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3987": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "3980": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "1614": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "359": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}, "285": {"$update": {"ARO_category": {"$insert": {"35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}}}}}}, "$delete": ["3349", "2885"], "$insert": {"5984": {"model_id": "5984", "ARO_accession": "3007645", "model_param": {"blastp_bit_score": {"param_value": "1040", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "CplR is an ABC-F ATPase ribosomal protection protein from Clostridium sporogenes which confers resistance to pleuromutilins and lincosamides.", "model_sequences": {"sequence": {"8706": {"dna_sequence": {"partial": "0", "sequence": "ATGGTATCAATAAAATTAGATAAAGTAAAAAAATATTATGAAGATAAATTAATTTTAGATATAGACAATTTAGAAATAAAAGAAAATAGTAGAATCGGAATTGTTGGAGAAAATGGAGCTGGTAAAACAACTCTTATTAAAGTTATTTTAGGTGAACTAGATATTGATGAGGGAAAAGTATTTTTTCATGCTAATTATTCATATATAAGCCAAAGTGAAAACTATACTGGTTCCTGCAATGATGGCAGAATCAAGAGTATATTAGGTGCACCAGATAATTATAATGAATTTTTATCCGGTGGAGAAAAGGTGAAAATTAGTATTAATCAAGCCCTTAGTTCTAATAGCAATTTTCTTATAGCAGATGAGCCAACAGCTAATCTTGACACTAATACTATAAAAAGCATTGAAAAACTTATAAGTGAATATAAAGGAGGACTTTTATTAGTTTCTCATGATAGAGATTTTTTAAATAATCTTTGTGATAATATATTAGAAATAGAAAATGGAAAAGTTAAATTATATAAGTGTGGTTATTCAAAATATCTTAAACTAAAAGCTAAAGAAAGAGAAGTTGAAAAAAGAGAATATGAAGAATATATAACTGAAAAAAAGCGACTTGAAAAGGCTATGATGGTAAAAAAAAATCAACAAGATTCTATTAGAAAAGCACCTAAAAGAATGGGAAATTCGGAAGCAAGACTTCATAAAATGGGAGATCAGAAATCAAAAAAACACTTAGATGGAAATATAAAATCTTTAAAAAGTAGAATTAATCATCTTGAAGTGAAAGAAAAACCTATTTCTAGCAAAGATATTAAGATAAAAATTACTGAAGGTAATAAAATACCTTCTAAAACAGTAATAGAAGTAAAAAATTTAGATTTATATATAGGTGATAAACTTCTTATAAAAGATGGAAATTTCAAAATAAAAAACGGTAAAAAAGCAGCTATTATTGGTGAAAATGGCTGTGGTAAAACAACTTTAATAAAAGAAATATTAAAAAGAGATACAGAAAACATTAGATTATCAAAGTATATTTCTATAGGATATTTTGATCAAAATCAAGACATTTTAGATAAAGACAAAACAATATTAGATAATATAAAATCAACTAGTTCTTATGATGAAAGCTTTATGAGAATACAATTAGCTGGATTTGGGTTTAAAGGAGACACTATATACAAAAATGTTTCTATATTAAGTGGAGGAGAAAAAGTTAAAGTTGCACTTTCCAAAATAATTTTAAGTGATACTAATACTTTGATTTTAGATGAACCTACCAATTATTTAGATATAAAATCTATTGAAGCTTTAGAAAATGCACTTATTAATACAGACAAAACAATTGTAATGATATCTCATGATAGATCTTTTATTTCTAGTATATGTAATTATATAATTGAAATAAAAGATACTAAACTAAATTGTTTTTCGGGTACTTATACTGCTTTCACTGAAGAAAGAGTAAACTATGAAACTAAAAAACAGGATAACCATAGTGAGCGTGAAAAGAAGGAAAAATTATTAATCTTAGAAAATAGACTTTCAAAAATAATTTCAGAAATATCTTTTGAGAAAGATTTGATAGTTAAAGAGAAGTTAAATGAGGAATATATTAAATTATTAAACGACATCAAATTATTAAAAAAGTAA", "fmax": "655537", "accession": "CP009225.1", "fmin": "653878", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium sporogenes", "NCBI_taxonomy_id": "1509", "NCBI_taxonomy_cvterm_id": "43756"}, "protein_sequence": {"accession": "AKC61310.1", "sequence": "MVSIKLDKVKKYYEDKLILDIDNLEIKENSRIGIVGENGAGKTTLIKVILGELDIDEGKVFFHANYSYISQSENYTGSCNDGRIKSILGAPDNYNEFLSGGEKVKISINQALSSNSNFLIADEPTANLDTNTIKSIEKLISEYKGGLLLVSHDRDFLNNLCDNILEIENGKVKLYKCGYSKYLKLKAKEREVEKREYEEYITEKKRLEKAMMVKKNQQDSIRKAPKRMGNSEARLHKMGDQKSKKHLDGNIKSLKSRINHLEVKEKPISSKDIKIKITEGNKIPSKTVIEVKNLDLYIGDKLLIKDGNFKIKNGKKAAIIGENGCGKTTLIKEILKRDTENIRLSKYISIGYFDQNQDILDKDKTILDNIKSTSSYDESFMRIQLAGFGFKGDTIYKNVSILSGGEKVKVALSKIILSDTNTLILDEPTNYLDIKSIEALENALINTDKTIVMISHDRSFISSICNYIIEIKDTKLNCFSGTYTAFTEERVNYETKKQDNHSEREKKEKLLILENRLSKIISEISFEKDLIVKEKLNEEYIKLLNDIKLLKK"}}}}, "model_name": "Clostridium sporogenes cplR", "ARO_category": {"35983": {"category_aro_name": "clindamycin", "category_aro_cvterm_id": "35983", "category_aro_accession": "0000066", "category_aro_class_name": "Antibiotic", "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."}, "37713": {"category_aro_name": "retapamulin", "category_aro_cvterm_id": "37713", "category_aro_accession": "3001314", "category_aro_class_name": "Antibiotic", "category_aro_description": "Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections."}, "45630": {"category_aro_name": "Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins", "category_aro_cvterm_id": "45630", "category_aro_accession": "3007068", "category_aro_class_name": "AMR Gene Family", "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."}, "37014": {"category_aro_name": "pleuromutilin antibiotic", "category_aro_cvterm_id": "37014", "category_aro_accession": "3000670", "category_aro_class_name": "Drug Class", "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."}, "35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "46411": {"category_aro_name": "iboxamycin", "category_aro_cvterm_id": "46411", "category_aro_accession": "3007636", "category_aro_class_name": "Antibiotic", "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."}, "46413": {"category_aro_name": "hygromycin A", "category_aro_cvterm_id": "46413", "category_aro_accession": "3007638", "category_aro_class_name": "Antibiotic", "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."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "Clostridium sporogenes cplR", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Cspo_cplR", "ARO_id": "46421", "model_type_id": "40292"}, "6006": {"model_id": "6006", "ARO_accession": "3003638", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "OXA-481 is a carbapenem-hydrolyzing class D beta-lactamase.", "model_sequences": {"sequence": {"8734": {"dna_sequence": {"partial": "1", "sequence": "ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAATTCATTAAAACAG", "fmax": "896", "accession": "KP264123.1", "fmin": "89", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKF41838.1", "sequence": "MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMNSLKQ"}}}}, "model_name": "OXA-481", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35973": {"category_aro_name": "oxacillin", "category_aro_cvterm_id": "35973", "category_aro_accession": "0000056", "category_aro_class_name": "Antibiotic", "category_aro_description": "Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis."}, "35930": {"category_aro_name": "cloxacillin", "category_aro_cvterm_id": "35930", "category_aro_accession": "0000011", "category_aro_class_name": "Antibiotic", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-481", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "OXA-481", "ARO_id": "40248", "model_type_id": "40292"}, "6007": {"model_id": "6007", "ARO_accession": "3000966", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "TEM-103 is an inhibitor-resistant beta-lactamase that has been found in E. coli.", "model_sequences": {"sequence": {"8735": {"dna_sequence": {"partial": "0", "sequence": "ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA", "fmax": "1005", "accession": "AAAGNS010000063.1", "fmin": "144", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Salmonella enterica subsp. enterica serovar Panama", "NCBI_taxonomy_id": "29472", "NCBI_taxonomy_cvterm_id": "35673"}, "protein_sequence": {"accession": "EAC0197234.1", "sequence": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"}}}}, "model_name": "TEM-103", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "36023": {"category_aro_name": "TEM beta-lactamase", "category_aro_cvterm_id": "36023", "category_aro_accession": "3000014", "category_aro_class_name": "AMR Gene Family", "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."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "35923": {"category_aro_name": "monobactam", "category_aro_cvterm_id": "35923", "category_aro_accession": "0000004", "category_aro_class_name": "Drug Class", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}}, "ARO_name": "TEM-103", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "TEM-103", "ARO_id": "37346", "model_type_id": "40292"}, "5988": {"model_id": "5988", "ARO_accession": "3007654", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8709": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTGCATATTCTCGTGGTCGTCACGAAAACGGCCAGAACTTTCTCACTGACTCCCGCGTTATCGCCTCTCTCTTGGAGCGTGTGGGAAGCACTAGCGGCCCCTTGATTGAGATTGGTCCCGGCCAAGGAGCGCTGACTCATCCGTTGTCTTGTACGGGACGATCTCTCACAGCTGTTGAAATTGACCCCGCGCTGGCAGGTGCGCTGCGGCGGGAACTTGACGATGCTGTGACTGTCATCAACGAAGATTTTCTGAGATACCGTCTGCCAGCCCACCCTCATGTGATTGTTGGTAACATCCCGTTTCATATCACCACATCCATCTTGCGGCGCCTTCTTCGCGCCCCAGGCTGGACCGACGCTGTGCTGCTTATGCAGTGGGAGGTTGCCCGCCGACGTGCTGGCGTCGGTGCGTCAACCATGATGACCGCCCAGTGGGCTCCGTGGTTCACTTTTGAGCTTGGAGAACGTGTTAGCCGGGAGGCGTTTACCCCTCGTCCTAGTGTGGATGGTGGCGTTTTGCACATCCGACGCCGTCCTAAAATGTTGGTACCAGTTGGAAAGCGAAAGGCGTTCCAAGCTCTAGTGCACGCCGTCTATACGGGGAAGGGTCGTGGGATCGTCGATATCGTCACCCAAGCGAAGATATTTCCCTCTCGACAGGCGGCGCGGAAATGGGCCGAGCGGTCCGGTGTGCATTCGCATCAGCTGCCCTCTGACCTGTCTGTTGCTCAGATGGTCAGCCTCTTCGAAAGCCGTGGGGCAGTTCCGCCGCGACGCCGCAAACAGAGGAAATAG", "fmax": "1287", "accession": "OQ326498.1", "fmin": "486", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Trueperella pyogenes", "NCBI_taxonomy_id": "1661", "NCBI_taxonomy_cvterm_id": "43836"}, "protein_sequence": {"accession": "WGG63489.1", "sequence": "MSAYSRGRHENGQNFLTDSRVIASLLERVGSTSGPLIEIGPGQGALTHPLSCTGRSLTAVEIDPALAGALRRELDDAVTVINEDFLRYRLPAHPHVIVGNIPFHITTSILRRLLRAPGWTDAVLLMQWEVARRRAGVGASTMMTAQWAPWFTFELGERVSREAFTPRPSVDGGVLHIRRRPKMLVPVGKRKAFQALVHAVYTGKGRGIVDIVTQAKIFPSRQAARKWAERSGVHSHQLPSDLSVAQMVSLFESRGAVPPRRRKQRK"}}}}, "model_name": "erm(56)", "ARO_category": {"36722": {"category_aro_name": "pristinamycin IA", "category_aro_cvterm_id": "36722", "category_aro_accession": "3000583", "category_aro_class_name": "Antibiotic", "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."}, "36699": {"category_aro_name": "Erm 23S ribosomal RNA methyltransferase", "category_aro_cvterm_id": "36699", "category_aro_accession": "3000560", "category_aro_class_name": "AMR Gene Family", "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."}, "35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "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."}, "35967": {"category_aro_name": "streptogramin B antibiotic", "category_aro_cvterm_id": "35967", "category_aro_accession": "0000050", "category_aro_class_name": "Drug Class", "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."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "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."}, "35983": {"category_aro_name": "clindamycin", "category_aro_cvterm_id": "35983", "category_aro_accession": "0000066", "category_aro_class_name": "Antibiotic", "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."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "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."}, "35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "erm(56)", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "erm(56)", "ARO_id": "46432", "model_type_id": "40292"}, "5989": {"model_id": "5989", "ARO_accession": "3007659", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8710": {"dna_sequence": {"partial": "0", "sequence": "ATGGCCAGCAGCCAGCTCGACAGGCAGAGGTCGCGGTCGGCCAAAATGAACCGCGCTCTGACAGCAGCAGAATGGTGGCGTCTGGGCCTGATGTTCGCGGTGATCGTCGCCTTGCATCTGGTTGGCTGGCTCACCGTGACGCTCTTGGTGGAGCCCGCGCGGCTCAGCTTGGGCGGCAAGGCATTCGGCATCGGCGTCGGGCTGACGGCGTACACGCTGGGCTTACGGCACGCGTTCGACGCCGACCACATCGCCGCCATCGACAACACCACCCGCAAGCTGATGAGCGACGGACACCGACCCCTTGCCGTCGGGTTCTTCTTTTCACTGGGCCACTCCACGGTGGTCTTCGGGCTGGCGGTAATGCTGGTGACCGGACTCAAGGCTATCGTCGGACCGGTCGAGAACGACTCCTCGACGCTGCATCACTACACAGGCTTGATCGGTACCAGCATTTCCGGCGCGTTCCTGTATTTGATCGGCATCCTCAACGTCATCGTCCTGGTCGGCATCGTGCGTGTCTTCGCCCACCTGCGCCGCGGCGACTACGACGAAGCCGAACTCGAACAGCAGTTGGACAACCGCGGACTGCTCATCCGGTTCCTCGGCCGCTTCACCAAGTCACTCACCAAGTCCTGGCATATGTACCCGGTCGGATTTTTGTTCGGTCTCGGGTTCGACACCGCCACCGAGATCGCGCTGTTGGTGCTGGCGGGAACCAGTGCCGCGGCCGGCCTGCCCTGGTATGCCATCCTGTGCCTGCCCGTCTTGTTCGCCGCCGGCATGTGTCTGCTGGACACCATCGACGGTTCGTTCATGAATTTCGCGTACGGCTGGGCCTTCTCCAGCCCCGTGCGCAAGATCTACTACAACATCACCGTCACCGGACTGTCGGTGGCAGTCGCACTGTTGATTGGCAGCGTTGAGCTGCTGGGCCTGATCGCCAACCAGTTGGGTTGGCAGGGCCCGTTCTGGGACTGGCTTGGCGGCCTCGACCTCAACACCGTCGGCTTCGTCGTCGTCGCGATGTTCGCGCTCACCTGGGCCATTGCCCTGCTGGTCTGGCACTACGGCCGCGTTGAAGAGCGGTGGACCCCGGCGCCCGACCGCACAACTTGA", "fmax": "3167802", "accession": "NC_000962.3", "fmin": "3166683", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "NP_217372.1", "sequence": "MASSQLDRQRSRSAKMNRALTAAEWWRLGLMFAVIVALHLVGWLTVTLLVEPARLSLGGKAFGIGVGLTAYTLGLRHAFDADHIAAIDNTTRKLMSDGHRPLAVGFFFSLGHSTVVFGLAVMLVTGLKAIVGPVENDSSTLHHYTGLIGTSISGAFLYLIGILNVIVLVGIVRVFAHLRRGDYDEAELEQQLDNRGLLIRFLGRFTKSLTKSWHMYPVGFLFGLGFDTATEIALLVLAGTSAAAGLPWYAILCLPVLFAAGMCLLDTIDGSFMNFAYGWAFSSPVRKIYYNITVTGLSVAVALLIGSVELLGLIANQLGWQGPFWDWLGGLDLNTVGFVVVAMFALTWAIALLVWHYGRVEERWTPAPDRTT"}}}}, "model_name": "putative nickel/cobalt transporter", "ARO_category": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "37007": {"category_aro_name": "ofloxacin", "category_aro_cvterm_id": "37007", "category_aro_accession": "3000663", "category_aro_class_name": "Antibiotic", "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."}, "37006": {"category_aro_name": "norfloxacin", "category_aro_cvterm_id": "37006", "category_aro_accession": "3000662", "category_aro_class_name": "Antibiotic", "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."}, "37005": {"category_aro_name": "nalidixic acid", "category_aro_cvterm_id": "37005", "category_aro_accession": "3000661", "category_aro_class_name": "Antibiotic", "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."}, "46133": {"category_aro_name": "gentamicin", "category_aro_cvterm_id": "46133", "category_aro_accession": "3007382", "category_aro_class_name": "Antibiotic", "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)."}, "37010": {"category_aro_name": "sparfloxacin", "category_aro_cvterm_id": "37010", "category_aro_accession": "3000666", "category_aro_class_name": "Antibiotic", "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."}, "36659": {"category_aro_name": "isoniazid", "category_aro_cvterm_id": "36659", "category_aro_accession": "3000520", "category_aro_class_name": "Antibiotic", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "45734": {"category_aro_name": "isoniazid-like antibiotic", "category_aro_cvterm_id": "45734", "category_aro_accession": "3007152", "category_aro_class_name": "Drug Class", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives."}, "46435": {"category_aro_name": "metal transporters with antibiotic efflux", "category_aro_cvterm_id": "46435", "category_aro_accession": "3007657", "category_aro_class_name": "AMR Gene Family", "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."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}}, "ARO_name": "putative nickel/cobalt transporter", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Rv2856", "ARO_id": "46437", "model_type_id": "40292"}, "6002": {"model_id": "6002", "ARO_accession": "3007669", "model_param": {"blastp_bit_score": {"param_value": "900", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8732": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAGCTACCAATCTTGATCCGAAACGCTGGTGGATATTGCTCGCTGTCGTGCTTGCATTTCTGCCGATTGTGATTGATATGACTGTACTGCATGTTGCGGTTCCCTCATTAACCCAATCGCTGAGTGCCACAAGTAACCAAGTCTTATGGATTATTGATATTTATCCATTACTTATGGCTGGACTTTTAGTTCCGATGGGAACTTTGGCTGATCGTGTCGGCAATCGTAAGATTCTGCTGATTGGCTTGGTTATATTTGGAATTGCCTCAGTCCTTGCGGCATTTTCCCAAACGGCTTCTATGCTGATTGCCGCACGTGCTTTATTAGCATTAGGCGGTGCCATGATTATGCCCTGTGTATTGGGTATTATTCGCAGAACCTTCGAAGACAGTCGCGAACGTGCCATTGCGCTGGGTATTTGGGGCACAATCGGATCAGCCGGTGCCGCCATTGGACCGCTCATTGGTGGGGGATTGTTAGAATATTTCTGGTGGGGTTCAGTTTTCCTGATTAACGTCCCAATCATGCTGGTTGTCGCACCAATGTGCTATTTCTTATTGTCCCGAAAAGAAGCTATAACCCCTGGACATTGGGCATTTGGTCAAGCGCTATTGCTGATTGTCGGTTTGATTTCGTTTGTATATGCACTAAAAGCAGGCTTAGGCGGTAAACAGTCGTTGTTGATTGTCTTGCCTTTGGTCGTTTTATCTATCGGCTTATTAACCATATTTGTACGCAAACAGCTGAATTCTCCTCAGCCGATGCTAGATCTTTCGCTATTTTCACGTCCTGCTATTTTAGCCGGCATTATTATGGCAATGGTTGCTGCAGGCGCTTTGGCAGGGGTTGAGTTAACTTTGGCAATGGAGCTGCAATATGTCATTCGTTTAACACCGCTGCAAGCCGGTCTTTTTATGGTTCCGATTATGGTTGCGGCCGCTATTGGCGGGCCTATTGCTGGTTTTTTATCCAATAAATTTGGACTCCGTCTGGTTGCGACCATGTCATTAATATTGGCAGCAATTGCGTTGGTCAGTTTGAGTTATTCAGATTTTCATCATCCGGGAATCATCGTTCCCTTTATTTTAGCTTCGATTGGATTAACACTGAGTATTGGTTTAACAGCTTCATCCATTGCGATCATGGGCTCAGTACCTGCAGAAAAGGGCGGTGCGGCAGGTTCACTTGAAAGTACAGGTTATGAACTGGGTACAGGACTAGGTATTACTTTATTTGGTGTTTTCATGGCCTATATATTTGGCAGTCATCTTCAAGTGCCGTCAGATTTAACTGCTGTTTTAGCAGAAAAAGCCAGACTTTCGATTGGTGATACCTATTTAGTGGCGAGCCAGTTACCCGTTGAACAAGGTACAGCATTGATTAACGCAGGTAAAATTGCCTTCAGTTCAGCTCATGTTAATTTATTATTAACAGCAGGGATTATCATCGGGATACTCTCCATTGTGGTATTTTTTATGCTAGCTAAATATCGAGATGAGAATTCATTGTGA", "fmax": "30619", "accession": "KT852971.1", "fmin": "29104", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AMD83542.1", "sequence": "MKATNLDPKRWWILLAVVLAFLPIVIDMTVLHVAVPSLTQSLSATSNQVLWIIDIYPLLMAGLLVPMGTLADRVGNRKILLIGLVIFGIASVLAAFSQTASMLIAARALLALGGAMIMPCVLGIIRRTFEDSRERAIALGIWGTIGSAGAAIGPLIGGGLLEYFWWGSVFLINVPIMLVVAPMCYFLLSRKEAITPGHWAFGQALLLIVGLISFVYALKAGLGGKQSLLIVLPLVVLSIGLLTIFVRKQLNSPQPMLDLSLFSRPAILAGIIMAMVAAGALAGVELTLAMELQYVIRLTPLQAGLFMVPIMVAAAIGGPIAGFLSNKFGLRLVATMSLILAAIALVSLSYSDFHHPGIIVPFILASIGLTLSIGLTASSIAIMGSVPAEKGGAAGSLESTGYELGTGLGITLFGVFMAYIFGSHLQVPSDLTAVLAEKARLSIGDTYLVASQLPVEQGTALINAGKIAFSSAHVNLLLTAGIIIGILSIVVFFMLAKYRDENSL"}}}}, "model_name": "aadT", "ARO_category": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36003": {"category_aro_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "category_aro_cvterm_id": "36003", "category_aro_accession": "0010002", "category_aro_class_name": "AMR Gene Family", "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."}, "45598": {"category_aro_name": "chlorhexidine", "category_aro_cvterm_id": "45598", "category_aro_accession": "3007039", "category_aro_class_name": "Antibiotic", "category_aro_description": "Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate)."}, "35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "43746": {"category_aro_name": "disinfecting agents and antiseptics", "category_aro_cvterm_id": "43746", "category_aro_accession": "3005386", "category_aro_class_name": "Drug Class", "category_aro_description": "Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance."}, "35968": {"category_aro_name": "tetracycline", "category_aro_cvterm_id": "35968", "category_aro_accession": "0000051", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome."}, "35925": {"category_aro_name": "erythromycin", "category_aro_cvterm_id": "35925", "category_aro_accession": "0000006", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "aadT", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "aadT", "ARO_id": "46449", "model_type_id": "40292"}, "6003": {"model_id": "6003", "ARO_accession": "3007671", "model_param": {"blastp_bit_score": {"param_value": "250", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8724": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTAAAGAAATGAGATTGAAAAAAAGAGAAATGACAAAAGAAGATACTGTTGAAGTATTAAAAAATGGTGAATTTGGTACTTTTTCCACTATATCTGAAAATGGTTATCCTTATGGAGTTGCTGTAAATTATGTATACTTTAATGATTCTATTTACTTTCATTGTGCAAGAAATGGACATAAGTTAGATAATATATCGAAAAACAACAAAGTTTCTTTTTTAGTAGTTGCTAATGAAAGTGTTATTCCAGATAAATTTAGTACTACTTATTCTAGTGCTATAGTTTTTGGAAAAGCTTGCACTGTAGAAAATGAAGAAAAGAAAAATGCTCTTGTAGAAATAATAAAAAAATATTCTAAAGGATTCTTTGAAGAAGGCATGAAGTACATAGAGAAGGATATGAACTTAACAACTGTTGTTAAAATAGAAATTGACCATATTTCTGGTAAAGCTTCACGTATATAA", "fmax": "1547941", "accession": "FN545816.1", "fmin": "1547473", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridioides difficile R20291", "NCBI_taxonomy_id": "645463", "NCBI_taxonomy_cvterm_id": "46452"}, "protein_sequence": {"accession": "CBE03766.1", "sequence": "MFKEMRLKKREMTKEDTVEVLKNGEFGTFSTISENGYPYGVAVNYVYFNDSIYFHCARNGHKLDNISKNNKVSFLVVANESVIPDKFSTTYSSAIVFGKACTVENEEKKNALVEIIKKYSKGFFEEGMKYIEKDMNLTTVVKIEIDHISGKASRI"}}}}, "model_name": "Clostridioides difficile nimB", "ARO_category": {"41239": {"category_aro_name": "nitroimidazole antibiotic", "category_aro_cvterm_id": "41239", "category_aro_accession": "3004115", "category_aro_class_name": "Drug Class", "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."}, "37033": {"category_aro_name": "metronidazole", "category_aro_cvterm_id": "37033", "category_aro_accession": "3000689", "category_aro_class_name": "Antibiotic", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "45671": {"category_aro_name": "nitroimidazole reductase", "category_aro_cvterm_id": "45671", "category_aro_accession": "3007103", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "Clostridioides difficile nimB", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "CdnimB", "ARO_id": "46451", "model_type_id": "40292"}, "6001": {"model_id": "6001", "ARO_accession": "3007662", "model_param": {"blastp_bit_score": {"param_value": "1300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "Rv1877, a putative Major Facilitator Superfamily efflux pump from M. tuberculosis actively effluxes fluoroquinolones ofloxacin and levofloxacin.", "model_sequences": {"sequence": {"8722": {"dna_sequence": {"partial": "0", "sequence": "ATGGCGGGCCCCACAGCACCGACCACTGCCCCCACCGCAATCCGAGCCGGTGGCCCGCTGCTCAGTCCGGTGCGACGCAACATTATTTTCACCGCACTTGTGTTCGGGGTGCTGGTCGCTGCGACCGGCCAAACCATCGTTGTGCCCGCATTGCCGACGATCGTCGCCGAGCTGGGCAGCACCGTTGACCAGTCGTGGGCGGTCACCAGCTATCTGCTGGGGGGAACTGTCGTGGTTGTGGTGGCTGGCAAGCTCGGTGATCTGCTCGGCCGCAACAGGGTGCTGCTAGGCTCCGTCGTGGTCTTCGTCGTTGGCTCTGTGCTGTGCGGGTTATCGCAGACGATGACCATGCTGGCGATCTCTCGCGCACTGCAGGGCGTCGGTGCCGGTGCGATTTCCGTCACCGCCTACGCGCTGGCCGCTGAGGTGGTCCCACTGCGGGACCGTGGCCGCTACCAGGGCGTCTTAGGTGCGGTGTTCGGTGTCAACACGGTCACCGGTCCGCTGCTGGGGGGCTGGCTCACCGACTATCTGAGCTGGCGGTGGGCGTTTTGGATCAACGTGCCGGTTTCGATCGCGGTGCTGACAGTGGCGGCAACCGCCGTCCCTGCGTTGGCCCGACCGCCCAAACCGGTCATCGACTACCTTGGGATCCTGGTCATCGCTGTGGCCACGACCGCTTTGATCATGGCCACAAGTTGGGGCGGAACCACCTACGCCTGGGGCTCAGCGACCATTGTCGGGCTGTTGATCGGGGCCGCAGTGGCGCTGGGTTTCTTCGTGTGGCTGGAGGGCCGCGCCGCTGCGGCCATCCTGCCGCCCAGGCTGTTTGGCAGCCCAGTATTTGCCGTGTGCTGCGTCCTGTCCTTCGTGGTCGGATTCGCGATGCTGGGTGCACTGACCTTCGTACCGATCTATCTGGGGTACGTGGACGGCGCGTCGGCGACCGCGTCAGGTCTGCGCACGTTGCCGATGGTGATCGGCCTGCTGATCGCCTCGACCGGGACGGGTGTCCTGGTCGGCCGGACGGGCCGCTACAAGATCTTCCCGGTCGCGGGGATGGCGCTGATGGCGGTTGCGTTCCTGCTGATGTCGCAGATGGACGAGTGGACGCCACCGCTGCTGCAATCGCTGTACCTGGTCGTCCTAGGTGCCGGCATCGGATTGTCCATGCAGGTGCTCGTTCTCATCGTGCAGAACACGTCGTCTTTCGAAGACCTCGGCGTCGCAACATCGGGTGTGACCTTCTTCCGGGTGGTCGGCGCCTCGTTTGGTACCGCAACATTCGGTGCGTTGTTCGTAAACTTCCTGGACCGAAGACTCGGTTCCGCGCTGACGTCGGGCGCCGTGCCTGTCCCGGCAGTGCCATCTCCGGCTGTCTTGCATCAGCTGCCCCAGAGCATGGCCGCCCCGATCGTGCGGGCATATGCCGAGTCGCTCACCCAGGTGTTCCTTTGCGCGGTCTCGGTCACGGTGGTCGGTTTCATCCTGGCGCTGTTGCTGCGAGAGGTACCGCTCACCGACATCCACGATGACGCCGACGACCTCGGCGACGGGTTCGGTGTGCCCAGAGCCGAATCGCCGGAGGATGTGTTGGAAATCGCGGTTCGGCGTATGCTGCCGAACGGGGTGCGACTGCGCGATATTGCGACACAACCCGGTTGCGGACTCGGCGTCGCCGAGCTGTGGGCCCTTCTGCGGATCTATCAATACCAGCGGCTGTTCGAGGCAGTACGGCTGACCGATATCGGTAGACACCTGCACGTGCCCTATCAGGTCTTTGAACCCGTCTTCGACCGTCTGGTCCAGACCGGCTACGCGGCACGCGACGGCGACATCTTGACGCTAACCCCGTCCGGGCACCGTCAGGTCGACTCCCTCGCAGTTTTGATCCGTCAGTGGCTGCTCGACCACTTGGCCGTGGCGCCCGGCTTGAAGCGACAGCCAGACCACCAATTCGAAGCCGCTCTGCAGCACGTCACCGACGCGGTGCTCGTTCAACGAGACTGGTATGAAGATCTGGGCGACCTGTCGGAATCACGCCAACTCGCGGCTACAACGTAG", "fmax": "2127967", "accession": "NC_000962.3", "fmin": "2125903", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "NP_216393.1", "sequence": "MAGPTAPTTAPTAIRAGGPLLSPVRRNIIFTALVFGVLVAATGQTIVVPALPTIVAELGSTVDQSWAVTSYLLGGTVVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCGLSQTMTMLAISRALQGVGAGAISVTAYALAAEVVPLRDRGRYQGVLGAVFGVNTVTGPLLGGWLTDYLSWRWAFWINVPVSIAVLTVAATAVPALARPPKPVIDYLGILVIAVATTALIMATSWGGTTYAWGSATIVGLLIGAAVALGFFVWLEGRAAAAILPPRLFGSPVFAVCCVLSFVVGFAMLGALTFVPIYLGYVDGASATASGLRTLPMVIGLLIASTGTGVLVGRTGRYKIFPVAGMALMAVAFLLMSQMDEWTPPLLQSLYLVVLGAGIGLSMQVLVLIVQNTSSFEDLGVATSGVTFFRVVGASFGTATFGALFVNFLDRRLGSALTSGAVPVPAVPSPAVLHQLPQSMAAPIVRAYAESLTQVFLCAVSVTVVGFILALLLREVPLTDIHDDADDLGDGFGVPRAESPEDVLEIAVRRMLPNGVRLRDIATQPGCGLGVAELWALLRIYQYQRLFEAVRLTDIGRHLHVPYQVFEPVFDRLVQTGYAARDGDILTLTPSGHRQVDSLAVLIRQWLLDHLAVAPGLKRQPDHQFEAALQHVTDAVLVQRDWYEDLGDLSESRQLAATT"}}}}, "model_name": "Rv1877", "ARO_category": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36003": {"category_aro_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "category_aro_cvterm_id": "36003", "category_aro_accession": "0010002", "category_aro_class_name": "AMR Gene Family", "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."}, "37007": {"category_aro_name": "ofloxacin", "category_aro_cvterm_id": "37007", "category_aro_accession": "3000663", "category_aro_class_name": "Antibiotic", "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."}, "35988": {"category_aro_name": "levofloxacin", "category_aro_cvterm_id": "35988", "category_aro_accession": "0000071", "category_aro_class_name": "Antibiotic", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}}, "ARO_name": "Rv1877", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Rv1877", "ARO_id": "46442", "model_type_id": "40292"}, "5982": {"model_id": "5982", "ARO_accession": "3007637", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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).", "model_sequences": {"sequence": {"8704": {"dna_sequence": {"partial": "0", "sequence": "ATGTTGTTAGTAAAAGTAGAAAATTTAAAGAAATATTATGCAGATAAATTAATTTTGGATATAGATAAACTTGAAATATTAGAAAATGACAAAATAGGTCTAGTTGGTTCAAATGGTCAAGGAAAAACAACATTATTAAAAGCAATATTGGGAGAAATAGAAATTGATGAAGGATATACTTACCTTACAGAAAGCTATTCTTATATAAGTCAGAGTGAAAATAATATTGAAACATGTGGTCATAGTAAGGAGAAGAGTCTTTTAAATGCTCCAGATAAATTTGAAGAACACTTATCAGGAGGGGAAAAGGTTAAGTTAAAAATAGCAGATGCGCTGAGTAATAAGAAAAATATCATAATAGCTGATGAGCCAACTTCAAACTTAGATAAAAAAAGCATTGGGGTTTTGGAAGATATGTTTAAAAGGCATGAGGGAGCATTATTATTAATATCTCATGATAGACGTTTTCTGGATGAGTTATGTACAACTATATTAGAACTAGAAGATGGAAAACTAAAAGCTTACAAAGGCAATTACACTGATTATTTAATGCAAAAAGATGAAGAAGTAAAAAGAGCTGATTTTGAGTATCAAGAATATGTTAAAGAGAAAAAAAGGCTTGAAAAAGCTCTTTTATATAAAAAAGCTTTAAGTGATGGCATAAGAAAAACACCAAAAAGAATGGGTAATTCAGAAGCTAGGTTGCACAAAATGGGTGGTCAGACTAATAAGAAAAAGTTGGACTCAAATGTGAAGGCTATAAAAAGCAGAATTGATAAACTTGAGGTAAAGAATAAACCTAAAGTTTCTAAAGAAATGAACATTAAGATTCAAGATGGTATGGAGATAATTAGCAAAAATCTAGTAGAGGTAAAAGATATGACTCTAAAGTTAGAAAATAAGCTCCTGTTAGATAATGTTTCCTTTAAGATAAAAAGAGGTAAAAAGATAGCATTATTAGGTGATAATGGGTGTGGAAAAAGTACTCTGATAAAAGAAATATTGGCTGATAAAAATGACAATATAAAAATAAATAACAAGGTAAAAGTAGGTTATTTTGACCAAAATCAAAGTTTATTAGATGAGGAAAAGAGTGTTCTATACAATACTAAAGTTAATAGTTCATTTGATGAATCTTTTATAAGGATAAACTTAAGCCTATTTGGGTTTAAAGGTGATGATGTCTACAAAAAAGTAAAAGTACTTAGTGGTGGAGAAAAGGTAAAAATAGCACTATGTAAAATAATATTGGAAGATAATAATTTTTTAGTATTTGATGAACCAACAAATTACTTAGATATAAAATCTATGGAAGCACTGGAAAAGGCACTGATAAATACTGATAAAACTATGCTTATAGTGTCTCATGATAGAGTATTTGTATCACATATTTGTAACTATATTATAGAGATAAAAGATGCTAAAATAAGGGAGTTTGATTGTAATTATGACGAATATACAATTAGCAGAAATAAAAAAACTCCTAGTAGAGAAAACCAAATCAAAAAAGAAAATCTTCTAGTATTAGAAAATAGACTTACAACTGTTATATCTATGTTATCTATAGAAAAAGATAATCTAAAAAAAGAATTGTATGAATCAGAATATAATGAATTACTAAAACAAATCAATAAATTAAAAAATAGCTTTTAG", "fmax": "2986419", "accession": "CP010905.2", "fmin": "2984766", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridioides difficile 630", "NCBI_taxonomy_id": "272563", "NCBI_taxonomy_cvterm_id": "37603"}, "protein_sequence": {"accession": "AJP12342.1", "sequence": "MLLVKVENLKKYYADKLILDIDKLEILENDKIGLVGSNGQGKTTLLKAILGEIEIDEGYTYLTESYSYISQSENNIETCGHSKEKSLLNAPDKFEEHLSGGEKVKLKIADALSNKKNIIIADEPTSNLDKKSIGVLEDMFKRHEGALLLISHDRRFLDELCTTILELEDGKLKAYKGNYTDYLMQKDEEVKRADFEYQEYVKEKKRLEKALLYKKALSDGIRKTPKRMGNSEARLHKMGGQTNKKKLDSNVKAIKSRIDKLEVKNKPKVSKEMNIKIQDGMEIISKNLVEVKDMTLKLENKLLLDNVSFKIKRGKKIALLGDNGCGKSTLIKEILADKNDNIKINNKVKVGYFDQNQSLLDEEKSVLYNTKVNSSFDESFIRINLSLFGFKGDDVYKKVKVLSGGEKVKIALCKIILEDNNFLVFDEPTNYLDIKSMEALEKALINTDKTMLIVSHDRVFVSHICNYIIEIKDAKIREFDCNYDEYTISRNKKTPSRENQIKKENLLVLENRLTTVISMLSIEKDNLKKELYESEYNELLKQINKLKNSF"}}}}, "model_name": "Clostridioides difficile cplR", "ARO_category": {"45630": {"category_aro_name": "Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins", "category_aro_cvterm_id": "45630", "category_aro_accession": "3007068", "category_aro_class_name": "AMR Gene Family", "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."}, "37013": {"category_aro_name": "virginiamycin M1", "category_aro_cvterm_id": "37013", "category_aro_accession": "3000669", "category_aro_class_name": "Antibiotic", "category_aro_description": "Virginiamycin M1 is a streptogramin A antibiotic."}, "35952": {"category_aro_name": "streptogramin A antibiotic", "category_aro_cvterm_id": "35952", "category_aro_accession": "0000034", "category_aro_class_name": "Drug Class", "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."}, "35964": {"category_aro_name": "lincomycin", "category_aro_cvterm_id": "35964", "category_aro_accession": "0000046", "category_aro_class_name": "Antibiotic", "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."}, "35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "46411": {"category_aro_name": "iboxamycin", "category_aro_cvterm_id": "46411", "category_aro_accession": "3007636", "category_aro_class_name": "Antibiotic", "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."}, "36174": {"category_aro_name": "nucleoside antibiotic", "category_aro_cvterm_id": "36174", "category_aro_accession": "3000034", "category_aro_class_name": "Drug Class", "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."}, "35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "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."}, "35983": {"category_aro_name": "clindamycin", "category_aro_cvterm_id": "35983", "category_aro_accession": "0000066", "category_aro_class_name": "Antibiotic", "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."}, "46414": {"category_aro_name": "A201A", "category_aro_cvterm_id": "46414", "category_aro_accession": "3007639", "category_aro_class_name": "Antibiotic", "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."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "Clostridioides difficile cplR", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "cplR", "ARO_id": "46412", "model_type_id": "40292"}, "5983": {"model_id": "5983", "ARO_accession": "3007644", "model_param": {"blastp_bit_score": {"param_value": "950", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "CplR is an ABC-F ATPase ribosomal protection protein from Clostridium perfringes which confers resistance to pleuromutilins and lincosamides.", "model_sequences": {"sequence": {"8705": {"dna_sequence": {"partial": "0", "sequence": "TTGACTTTTTATGACTATATATACTCTCCTGTAATTTATAGGAGGGATTTTTTTATGTCTTTAGCAAGATTAAATAAAGTAAAAAAATATTATGGAGATAAATTAATTCTAGATATAGATAAACTAGAAATTTTAGATGAAGATAGAATCGGATTAGTTGGAGTTAATGGTGCTGGTAAAACTACACTTATTAAATCTTTATTAGGTCAAATTCCTATTGATGAAGGAAATGTATCTCTAACTAAAAGCTTTGCTTATATAAGTCAAAGTGAAAATTCTAATGAAGAAACTTTAAATAATAATTTTAAGAATGTATTCAATGCTCCTTTTGAATACCATGAGTTTTTATCAGGTGGAGAAAAGGTTAAATTTAAAATAGCTAAAGCTCTAGGTGAAAATAAACATTTAATTATTGCTGATGAGCCTACTGCTAATTTAGATGAAAACAGCATTGAAACTCTTGAAAACATGCTAAAAAACTATAATGGTGCATTACTTCTAGTATCACATGATAGAAGATTTCTAGATTCATTATGTAACACTATTATTGAAATTGAAGATGGAAAAATAAAAACTTATAAAGGAAATTTCTCTAAATATCTAGAGCTAAAAACTTTAGAGAGGCAAAGAGCTGAAATTGAGTATAATTCTTATATAAATGAAAAAAAGCATCTTGAAAATGCTATCCTTAATAAGCGAAACTTAAAAGATAGTCTTCGAAAAACACCTAAAAGAATGGGTAATTCTGAAGCTAGATTACACAAAATGGGGCCTCAAAGAGCAAAGAAAAATCTAGATAATAATATAAAGGCCTTAAGAAGTAGAATTGATCATCTTGACATTAAGGAAAAGCCTAAAACAATAAAAGAGATTAAAATTAGAGTTCAAGATAATTTAAAAATAGCTTCTAAAAATCTTATAGAAGCTAAAGATTTCACATTATTTGCAGGTAATAAGCTTCTACTTAAAGATATTAAATTTAAAATAAAGAATGGTAAGAAAGTAGCACTTATTGGTGATAATGGTTGTGGTAAAAGTACATTGCTAAAAAATATTATTTCAAAAGAAGACAATATAAAAGTTTTAGATAATGTTGTTATAGGCTACTTTGATCAATCTCAAAAGATATTAAAAGATGATGAATCAATACTAAAAAATATTCTTAAAGATTGTTCTTATGATGAAAATTTTGTGAGAATAAATCTAGATGGTTTTGGTTTTAAAGGAGATGATGTATTTAAGAAAGTCTCTTCCTTAAGTGGTGGTGAAAAAGTAAAAATAGCACTTTGTAAAATATTATTATCTGATAATAACTTAATAATATTGGACGAACCTACAAACTATCTTGACATAAAATCTATGGAATCTCTAGAGACTGCATTGATTAATTGTAATAAAACATTAATTGTAGTTTCTCATGATAGAAACTTTATTTCTAATGTATGCGATTATATTTTAGAGATAGATAACAATTTAATTCATGAATTTTCTGGCACCTATGATGAATATATAAAATTTAAGAAAAAACCTAAGTTAGATGATAAAGAAAGAGCTAATAAAGATAGTCTTCTTCTCTTAGAAAACAGACTTTCTAATGTAATATCGCTCCTTTCAATAGAACCTGACAACAATAAAAAAAGTTTATTAGAAAATGAATATTATAATTTACTTAAAGAATTAAAAAACTTAAGAAAAAGATTAAGTTAA", "fmax": "968935", "accession": "BA000016.3", "fmin": "967228", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium perfringens str. 13", "NCBI_taxonomy_id": "195102", "NCBI_taxonomy_cvterm_id": "46420"}, "protein_sequence": {"accession": "BAB80490.1", "sequence": "MTFYDYIYSPVIYRRDFFMSLARLNKVKKYYGDKLILDIDKLEILDEDRIGLVGVNGAGKTTLIKSLLGQIPIDEGNVSLTKSFAYISQSENSNEETLNNNFKNVFNAPFEYHEFLSGGEKVKFKIAKALGENKHLIIADEPTANLDENSIETLENMLKNYNGALLLVSHDRRFLDSLCNTIIEIEDGKIKTYKGNFSKYLELKTLERQRAEIEYNSYINEKKHLENAILNKRNLKDSLRKTPKRMGNSEARLHKMGPQRAKKNLDNNIKALRSRIDHLDIKEKPKTIKEIKIRVQDNLKIASKNLIEAKDFTLFAGNKLLLKDIKFKIKNGKKVALIGDNGCGKSTLLKNIISKEDNIKVLDNVVIGYFDQSQKILKDDESILKNILKDCSYDENFVRINLDGFGFKGDDVFKKVSSLSGGEKVKIALCKILLSDNNLIILDEPTNYLDIKSMESLETALINCNKTLIVVSHDRNFISNVCDYILEIDNNLIHEFSGTYDEYIKFKKKPKLDDKERANKDSLLLLENRLSNVISLLSIEPDNNKKSLLENEYYNLLKELKNLRKRLS"}}}}, "model_name": "Clostridium perfringes cplR", "ARO_category": {"37713": {"category_aro_name": "retapamulin", "category_aro_cvterm_id": "37713", "category_aro_accession": "3001314", "category_aro_class_name": "Antibiotic", "category_aro_description": "Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections."}, "45630": {"category_aro_name": "Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins", "category_aro_cvterm_id": "45630", "category_aro_accession": "3007068", "category_aro_class_name": "AMR Gene Family", "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."}, "37013": {"category_aro_name": "virginiamycin M1", "category_aro_cvterm_id": "37013", "category_aro_accession": "3000669", "category_aro_class_name": "Antibiotic", "category_aro_description": "Virginiamycin M1 is a streptogramin A antibiotic."}, "37014": {"category_aro_name": "pleuromutilin antibiotic", "category_aro_cvterm_id": "37014", "category_aro_accession": "3000670", "category_aro_class_name": "Drug Class", "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."}, "35952": {"category_aro_name": "streptogramin A antibiotic", "category_aro_cvterm_id": "35952", "category_aro_accession": "0000034", "category_aro_class_name": "Drug Class", "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."}, "35964": {"category_aro_name": "lincomycin", "category_aro_cvterm_id": "35964", "category_aro_accession": "0000046", "category_aro_class_name": "Antibiotic", "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."}, "35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "46411": {"category_aro_name": "iboxamycin", "category_aro_cvterm_id": "46411", "category_aro_accession": "3007636", "category_aro_class_name": "Antibiotic", "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."}, "35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "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."}, "35983": {"category_aro_name": "clindamycin", "category_aro_cvterm_id": "35983", "category_aro_accession": "0000066", "category_aro_class_name": "Antibiotic", "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."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "Clostridium perfringes cplR", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Cper_cplR", "ARO_id": "46419", "model_type_id": "40292"}, "5980": {"model_id": "5980", "ARO_accession": "3007633", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8702": {"dna_sequence": {"partial": "0", "sequence": "ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA", "fmax": "982", "accession": "NG_080778.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "WP_248496376.1", "sequence": "MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"}}}}, "model_name": "KPC-125", "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35923": {"category_aro_name": "monobactam", "category_aro_cvterm_id": "35923", "category_aro_accession": "0000004", "category_aro_class_name": "Drug Class", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "36198": {"category_aro_name": "KPC beta-lactamase", "category_aro_cvterm_id": "36198", "category_aro_accession": "3000059", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "KPC-125", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "KPC-125", "ARO_id": "46407", "model_type_id": "40292"}, "5981": {"model_id": "5981", "ARO_accession": "3007635", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8703": {"dna_sequence": {"partial": "0", "sequence": "ATGATACAAAGAAGACAGTTTTCCTTGGGTTTGGCATGGACCGCCATCGGGTCTCTGGCCGGATGCGCCGCAGGCCCCAGTGCTGCGGCGAAAACCGAGCGCCACTGGTCCCACGCCATGGCGCAAATTGAACAGGACGCGCAAGGCCGCCTGGGTGTGGCAATGCTGGACACAGGCAGTGGCCTGGCACTGGGGTGGAGACAGGACGAACGCTTTGCCATGTGCAGCACTTTCAAGCTCCCCTTGGCGGCCTGGGTGCTGGCACTGGTCGACCAAGGTCGTGAGCGCTTGGACGCACGCGTGCAGTACTCCGAGGCGGAGCTGGTGGAGTATTCCCCCGTCAGCGGCCCGAAAGCGGGTGCACGGGGCGGGCTGACCGTGGGCGAGCTGTGCGCCGCGACAGTGAGCCTGAGCGACAACTCCGCAGCCAACGTGCTGCTTGCACGCCATGGCGGCCCCGCTGCGCTGACGGCTTGGCTGCGCTCGCAAGGGGACTCCATCACACGACTGGATCGCAATGAGCCCTCATTAAACGAAGCCACCGTGGGCGATGAGCGCGACACCACCACACCACTTGCCATGCTTCATACCATGCAACGGCTGGTCCTGGGCAATTCACTGTCACCCTCATCACGCGCAACGCTACAACGCTGGCTGATCGAGACCAGCACGGGGGACCAACGCCTGCGGGCAGGCGCACCAGGTTGGAAAGTGGGCGACAAGACGGGCACCTCTGGCAGCAGTGGCACCGCGAACGACATTGGGGTGCTGTGGCCACCGGCAGGCGGCGCCCCGGTACTGGTGAGTTGCTACCTCACACAGTCCACAGCCCGCCCCGAGCAGCGCGATGCCGCCATCGCCCAGGTCGCCCGCGCTGTGTTGGCGGCGCGACAGTATCAGGCGCAATAG", "fmax": "16602", "accession": "CP079746.1", "fmin": "15693", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Comamonas aquatica", "NCBI_taxonomy_id": "225991", "NCBI_taxonomy_cvterm_id": "46410"}, "protein_sequence": {"accession": "QXW20276.1", "sequence": "MIQRRQFSLGLAWTAIGSLAGCAAGPSAAAKTERHWSHAMAQIEQDAQGRLGVAMLDTGSGLALGWRQDERFAMCSTFKLPLAAWVLALVDQGRERLDARVQYSEAELVEYSPVSGPKAGARGGLTVGELCAATVSLSDNSAANVLLARHGGPAALTAWLRSQGDSITRLDRNEPSLNEATVGDERDTTTPLAMLHTMQRLVLGNSLSPSSRATLQRWLIETSTGDQRLRAGAPGWKVGDKTGTSGSSGTANDIGVLWPPAGGAPVLVSCYLTQSTARPEQRDAAIAQVARAVLAARQYQAQ"}}}}, "model_name": "CAE-1", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35975": {"category_aro_name": "cefazolin", "category_aro_cvterm_id": "35975", "category_aro_accession": "0000058", "category_aro_class_name": "Antibiotic", "category_aro_description": "Cefazolin (INN), 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."}, "35980": {"category_aro_name": "cefuroxime", "category_aro_cvterm_id": "35980", "category_aro_accession": "0000063", "category_aro_class_name": "Antibiotic", "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."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "46408": {"category_aro_name": "CAE beta-lactamase", "category_aro_cvterm_id": "46408", "category_aro_accession": "3007634", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CAE beta-lactamases are a novel class A serine beta-lactamase family first isolated from Comamonas aquatica."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "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."}, "35979": {"category_aro_name": "ceftriaxone", "category_aro_cvterm_id": "35979", "category_aro_accession": "0000062", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "CAE-1", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "CAE-1", "ARO_id": "46409", "model_type_id": "40292"}, "5986": {"model_id": "5986", "ARO_accession": "3007648", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8707": {"dna_sequence": {"partial": "0", "sequence": "GTGAAATTGATTTCTCAAACATTGATAGCAACAGCGCTGACCTCGGCGTGCTCCATGGCGTTTGCCACCACGGCAGATGTGCAAGCAACCGTTGATCGGGCGATCAAACCGCTAATGCAGCAGCAATCGATTCCCGGCATGGCGGTAGCGGTGGTGATTAAAGGCCAGCCGCACTATTTCACCTGGGGCATGGCGGATGTCAAACAGCAGCGCCCGGTCACCCAAGACACGCTGTTTGAGCTGGGTTCGGTGAGTAAAACCTTCACCGGCGTGCTAGGTGGCGTCGCGGTGAATAAAGGCGAGATCGCGCTGAGCGATGCTGCCAGCAAATATTGGCCGGCACTGAATACGCCGCAGTGGCGCGACACCACGCTGCTGCAGCTGGCGACTTACACCGCTGGCGGCTTGCCGCTGCAGGTGCCCGATGCCGTGACCGATGAAAAGGCGCTGGCGAACTTCTATCAACAATGGCAACCACAATGGACGCCGGGCAGCACGCGTCAATATGCCAACAGCAGCATCGGCTTATTTGGCTGGCTGGCGACGAAACCCAGCGGGCTTACTTTTGAACAGGCAATGCAGCAGCGCGTATTCACGCCATTGCAGCTCAAGCACACCTTTATCACCGTGCCTGACGCCGCGAAAAACGCTTACGCATGGGGCTACCGCGAAGGCAAACCGGTGCGCGTGTCGCCGGGCATGCTGGATGCTGAAGCCTATGGCGTGAAGTCGTCGGTTAAAGATATGGCGCGCTGGATGCAGGCCAATATGGATCCGCAGCAGGTTAACGATAAGCCGCTGCAGCAGGCGCTGGATTTCGCGCAAACGCGTTTCTATCGCACCGATGCGCTCTATCAAGGTTTGGGGTGGGAGATGCTGGATTGGCCCGCTCAGGCGGAGATGGCGGTGAAGGGCGCGGATAACAAGGTGGCGCTTGGGCCGCAGCCGGTGCGGGATGCCGAATCACATCCGCGTGTCAGCGCGTCGTGGGTGCATAAGACCGGCGCAACCGGTGGGTTCGGTGCTTATGTCGCCTTCATCCCGGAGAAGCAGGTCGGCATTGTGATATTGGCAAACAAAAATTATCCCAATACCGAGCGGGTTAAAGCCGCGATGCAGATTCTGAAAGCGTTGCAGTAA", "fmax": "1342", "accession": "OQ725878.1", "fmin": "202", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pantoea sp.", "NCBI_taxonomy_id": "69393", "NCBI_taxonomy_cvterm_id": "46425"}, "protein_sequence": {"accession": "WGF22896.1", "sequence": "MKLISQTLIATALTSACSMAFATTADVQATVDRAIKPLMQQQSIPGMAVAVVIKGQPHYFTWGMADVKQQRPVTQDTLFELGSVSKTFTGVLGGVAVNKGEIALSDAASKYWPALNTPQWRDTTLLQLATYTAGGLPLQVPDAVTDEKALANFYQQWQPQWTPGSTRQYANSSIGLFGWLATKPSGLTFEQAMQQRVFTPLQLKHTFITVPDAAKNAYAWGYREGKPVRVSPGMLDAEAYGVKSSVKDMARWMQANMDPQQVNDKPLQQALDFAQTRFYRTDALYQGLGWEMLDWPAQAEMAVKGADNKVALGPQPVRDAESHPRVSASWVHKTGATGGFGAYVAFIPEKQVGIVILANKNYPNTERVKAAMQILKALQ"}}}}, "model_name": "PSZ-1", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "46423": {"category_aro_name": "PSZ beta-lactamase", "category_aro_cvterm_id": "46423", "category_aro_accession": "3007647", "category_aro_class_name": "AMR Gene Family", "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."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35975": {"category_aro_name": "cefazolin", "category_aro_cvterm_id": "35975", "category_aro_accession": "0000058", "category_aro_class_name": "Antibiotic", "category_aro_description": "Cefazolin (INN), 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."}, "36976": {"category_aro_name": "benzylpenicillin", "category_aro_cvterm_id": "36976", "category_aro_accession": "3000632", "category_aro_class_name": "Antibiotic", "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."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "35981": {"category_aro_name": "amoxicillin", "category_aro_cvterm_id": "35981", "category_aro_accession": "0000064", "category_aro_class_name": "Antibiotic", "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."}, "35927": {"category_aro_name": "cefoxitin", "category_aro_cvterm_id": "35927", "category_aro_accession": "0000008", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "PSZ-1", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "PSZ-1", "ARO_id": "46424", "model_type_id": "40292"}, "5987": {"model_id": "5987", "ARO_accession": "3007650", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8708": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAATCCCTCTGCCTGACGCTGCTGCTCGCCGCCTCATGCTCTACTTTTGCCGCGCCAAAGCAGCTTACCGCGCAGCAGATCGAAAAAATCGTTAATCGCACGATTTCGCCGCTGCTGAAAGAGCAGGCGATCCCGGGTATGGCAGTCGCCGTTATCTATAAAGGCTACCCGCTGTATTTCACCTGGGGCAAAGCCGACGTGCAGCATAACGAACCGGTAACCCGGCAAACTCTGTTCGAGCTTGGTTCTGTAAGTAAAACATTTACCGGCGTGCTGGGCGGGGATACGCTGGCTCGCGGCGAGATAAGCCTTAGCGATCCGGCGCAAAAATATTGGCCAGAGCTAACCGGCAGCCAGTGGAAAGGAATAACGCTATTGCAACTGGCAACCTATACAGCAGGCGGGTTGCCGCTACAGGTGCCTGATGAAGTTACCGACAGCGCCTCGCTGCTCAACTTTTACCAGTCATGGCAGCCGCAGTGGGCACCAGGCAGCAAAAGGCTCTATGCCAACGCCAGCATTGGGTTGTTTGGGGCGTTGATGGTTAAGCCTTCAGGAATGGGCTTCGAGCAGGCGATGACAACGCGAGTGCTGGAACCATTGAAGCTGGCTCATACCTGGATAACCGTTCCTCCCGCTGAAGAGAGCCATTACGCCTGGGGCTACCGCAACGACAAAGCGGTACGCGTTTCACCGGGCATGCTGGATGCAGAAGCCTACGGCGTTAAGTCCAGCATCGAAGATATGGCGCACTGGGTGCAGGCGAATATGGTGCCGGAGCGGGTGGAAGACCAAAATCTGCAACAGGGGATCAAACTTGCTCAGTCTCGCTACTGGCGGATTGGCAGCATGTATCAGGGTCTGGGCTGGGAAATGCTGAACTGGCCGCTGAAGGGCAAAGTGATTATCGACGGCAGCGATAATAAAGTCGCCCTTGCCCCGCAGACCGCGGTCGCTATTGACCCACCGGCCCCGCTAGTGAAGGCATCCTGGGTACACAAAACTGGCTCAACCGGCGGCTTCGGTAGCTATGTGGCCTTTATTCCCGAAAAGCAGTTGGGCATCGTGATGCTGGCGAACAAAAGCTACCCGAATCCTGAGCGGGTAAAAGCCGCCTACGCTATTCTCGAAGCGCTGCAATAA", "fmax": "1149", "accession": "KJ650399.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Cedecea davisae", "NCBI_taxonomy_id": "158484", "NCBI_taxonomy_cvterm_id": "46428"}, "protein_sequence": {"accession": "AID52933.1", "sequence": "MKKSLCLTLLLAASCSTFAAPKQLTAQQIEKIVNRTISPLLKEQAIPGMAVAVIYKGYPLYFTWGKADVQHNEPVTRQTLFELGSVSKTFTGVLGGDTLARGEISLSDPAQKYWPELTGSQWKGITLLQLATYTAGGLPLQVPDEVTDSASLLNFYQSWQPQWAPGSKRLYANASIGLFGALMVKPSGMGFEQAMTTRVLEPLKLAHTWITVPPAEESHYAWGYRNDKAVRVSPGMLDAEAYGVKSSIEDMAHWVQANMVPERVEDQNLQQGIKLAQSRYWRIGSMYQGLGWEMLNWPLKGKVIIDGSDNKVALAPQTAVAIDPPAPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPERVKAAYAILEALQ"}}}}, "model_name": "CDA-1", "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "41256": {"category_aro_name": "cephaloridine", "category_aro_cvterm_id": "41256", "category_aro_accession": "3004129", "category_aro_class_name": "Antibiotic", "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."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "40523": {"category_aro_name": "ticarcillin", "category_aro_cvterm_id": "40523", "category_aro_accession": "3003832", "category_aro_class_name": "Antibiotic", "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."}, "40955": {"category_aro_name": "ticarcillin-clavulanic acid", "category_aro_cvterm_id": "40955", "category_aro_accession": "3004023", "category_aro_class_name": "Antibiotic+Adjuvant", "category_aro_description": "An antibiotic cocktail containing the beta-lactam antibiotic ticarcillin and the beta-lactamase inhibitor clavulanic acid (clavulanate)."}, "46426": {"category_aro_name": "CDA beta-lactamase", "category_aro_cvterm_id": "46426", "category_aro_accession": "3007649", "category_aro_class_name": "AMR Gene Family", "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."}, "35996": {"category_aro_name": "clavulanic acid", "category_aro_cvterm_id": "35996", "category_aro_accession": "0000079", "category_aro_class_name": "Adjuvant", "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."}, "35927": {"category_aro_name": "cefoxitin", "category_aro_cvterm_id": "35927", "category_aro_accession": "0000008", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "CDA-1", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "CDA-1", "ARO_id": "46427", "model_type_id": "40292"}, "6008": {"model_id": "6008", "ARO_accession": "3000930", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "TEM-61 is an extended-spectrum beta-lactamase that has been found in clinical isolates.", "model_sequences": {"sequence": {"8736": {"dna_sequence": {"partial": "0", "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA", "fmax": "3340", "accession": "LC542923.1", "fmin": "2479", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia marcescens", "NCBI_taxonomy_id": "615", "NCBI_taxonomy_cvterm_id": "36783"}, "protein_sequence": {"accession": "BCD58813.1", "sequence": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"}}}}, "model_name": "TEM-61", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "36023": {"category_aro_name": "TEM beta-lactamase", "category_aro_cvterm_id": "36023", "category_aro_accession": "3000014", "category_aro_class_name": "AMR Gene Family", "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."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "35923": {"category_aro_name": "monobactam", "category_aro_cvterm_id": "35923", "category_aro_accession": "0000004", "category_aro_class_name": "Drug Class", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}}, "ARO_name": "TEM-61", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "TEM-61", "ARO_id": "37310", "model_type_id": "40292"}, "6009": {"model_id": "6009", "ARO_accession": "3002447", "model_param": {"blastp_bit_score": {"param_value": "525", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "OKP-B-14 is a beta-lactamase found in Klebsiella pneumoniae.", "model_sequences": {"sequence": {"8737": {"dna_sequence": {"partial": "1", "sequence": "TGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCTGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTACGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATC", "fmax": "827", "accession": "DQ995288.1", "fmin": "2", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "ABL75154.1", "sequence": "CLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQLLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALI"}}}}, "model_name": "OKP-B-14", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "38817": {"category_aro_name": "OKP beta-lactamase", "category_aro_cvterm_id": "38817", "category_aro_accession": "3002417", "category_aro_class_name": "AMR Gene Family", "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%."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}}, "ARO_name": "OKP-B-14", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "OKP-B-14", "ARO_id": "38847", "model_type_id": "40292"}, "5969": {"model_id": "5969", "ARO_accession": "3007527", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13023": "A77T", "13022": "C85G", "13027": "G83A", "13026": "G83C", "13025": "G64C", "13029": "G83T", "13028": "C88G", "13030": "G73T", "13031": "A67G", "13032": "G89C"}, "clinical": {"13023": "A77T", "13022": "C85G", "13027": "G83A", "13026": "G83C", "13025": "G64C", "13029": "G83T", "13028": "C88G", "13030": "G73T", "13031": "A67G", "13032": "G89C"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}, "40330": {"param_value": {"13024": "G82T,G86T"}, "param_type_id": "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."}}, "ARO_description": "Amino acid substitutions in ribosomal protein S5, rpsE, is associated with resistance to spectinomycin (SpcR).", "model_sequences": {"sequence": {"8692": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTCGTATTGACCCAAGCAAATTAGAGTTAGAAGAACGCTTAGTTACGGTTAACCGCGTAGCGAAAGTTGTTAAAGGTGGTCGTCGTTTCCGCTTCGCAGCTCTAGTCGTTGTCGGTGACAAAAACGGACACGTAGGATTCGGTACTGGTAAAGCACAAGAAGTACCAGAAGCGATTCGCAAAGCTGTTGAAGATGCGAAAAAGAATTTGATTGAAGTACCAATGGTTGGAACTACAATTCCACACGAAATCATCGGACGTTTCGGTGCAGGTAACATCTTGTTAAAACCTGCTTCTGAAGGTACTGGAGTTATCGCTGGAGGCCCTGTACGTGCGGTACTTGAGCTAGCTGGTGTAGCTGATATCCTTTCTAAGTCTTTAGGTTCTAACACACCGATCAACATGATTCGTGCAACACTTCAAGGTTTAAGTGAACTTAAACGTGCTGAAGACGTTGCGAAGCTTCGTGGAAAATCTGTAGAAGAACTGTTAGGATAA", "fmax": "143861", "accession": "NC_000964.3", "fmin": "143360", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacillus subtilis subsp. subtilis str. 168", "NCBI_taxonomy_id": "224308", "NCBI_taxonomy_cvterm_id": "39579"}, "protein_sequence": {"accession": "NP_388014.1", "sequence": "MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAIRKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGVADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG"}}}}, "model_name": "Bacillus subtilis rpsE mutations conferring resistance to spectinomycin", "ARO_category": {"35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35957": {"category_aro_name": "spectinomycin", "category_aro_cvterm_id": "35957", "category_aro_accession": "0000039", "category_aro_class_name": "Antibiotic", "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."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}, "46297": {"category_aro_name": "spectinomycin resistant rpsE", "category_aro_cvterm_id": "46297", "category_aro_accession": "3007526", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "Bacillus subtilis rpsE mutations conferring resistance to spectinomycin", "model_type": "protein variant model", "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.", "CARD_short_name": "Bsub_rpsE_SPT", "ARO_id": "46298", "model_type_id": "40293"}, "5960": {"model_id": "5960", "ARO_accession": "3007476", "model_param": {"blastp_bit_score": {"param_value": "100", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"12938": "A64P", "12937": "D29A"}, "clinical": {"12938": "A64P", "12937": "D29A"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "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.", "model_sequences": {"sequence": {"8682": {"dna_sequence": {"partial": "0", "sequence": "ATGGCGGACCCCACAATTGTTGCTGGTGCCCTCATCGGTGGTGGGTTGATCATGGCCGGAGGCGCCATCGGTGCCGGTATCGGTGACGGTATCGCCGGTAACGCTCTGATCTCCGGTGTGGCTCGTCAGCCCGAGGCTCAGGGCCGGCTGTTCACCCCGTTCTTCATCACCGTCGGTCTGGTTGAGGCTGCGTACTTCATCAACCTGGCCTTCATGGCGTTGTTCGTCTTCGCGACTCCCGGCGCCAGCTAA", "fmax": "343", "accession": "DQ306899.1", "fmin": "91", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacteroides abscessus", "NCBI_taxonomy_id": "36809", "NCBI_taxonomy_cvterm_id": "36888"}, "protein_sequence": {"accession": "ABC24999.1", "sequence": "MADPTIVAGALIGGGLIMAGGAIGAGIGDGIAGNALISGVARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPGAS"}}}}, "model_name": "Mycobacterium abscessus atpE with mutation conferring resistance to bedaquiline", "ARO_category": {"35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "46244": {"category_aro_name": "antibiotic resistant ATP synthase", "category_aro_cvterm_id": "46244", "category_aro_accession": "3007477", "category_aro_class_name": "AMR Gene Family", "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."}, "41932": {"category_aro_name": "diarylquinoline antibiotic", "category_aro_cvterm_id": "41932", "category_aro_accession": "3004491", "category_aro_class_name": "Drug Class", "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."}, "41933": {"category_aro_name": "bedaquiline", "category_aro_cvterm_id": "41933", "category_aro_accession": "3004492", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "Mycobacterium abscessus atpE with mutation conferring resistance to bedaquiline", "model_type": "protein variant model", "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.", "CARD_short_name": "Mabs_atpE_BDQ", "ARO_id": "46243", "model_type_id": "40293"}, "5961": {"model_id": "5961", "ARO_accession": "3007491", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"12939": "D135N", "12940": "D135G"}, "clinical": {"12939": "D135N", "12940": "D135G"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "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.", "model_sequences": {"sequence": {"8683": {"dna_sequence": {"partial": "0", "sequence": "TTGGTTCGACCCCATTTGCCGCTGAACGCCCTGCGCGCCTTCGAAGCTTCGGCCCGGCACCTGAGCTTCACCCGCGCGGCCATCGAGCTGTGCGTGACCCAGGCGGCGGTCAGCCACCAGGTGAAGAGCCTCGAGGAGCGTCTCGGCGTGGCCCTGTTCAAGCGTCTGCCGCGCGGCCTCATGCTGACCCACGAGGGCGAGAGCCTGCTGCCGGTGCTGTGTGACTCCTTCGACCGCATCGCCGGCCTGCTGGAACGTTTCGAGGGTGGCCACTACCGGGACGTGCTCACCGTCGGCGCGGTCGGAACCTTCACGGTCGGTTGGCTGCTGCCGCGGCTGGAGGACTTCCAGGCGCGCCATCCCTTCATCGATCTGCGCCTGTCCACCCACAACAACCGCGTCGACATCGCCGCCGAGGGGCTCGACTACGCGATCCGCTTCGGCGGCGGCGCCTGGCACGGCACCGAGGCGCTGGCGTTGTTCGAGGCGCCGCTGACGGTGCTCTGCTGCCCGGAGGTCGCCGCCCAGTTGCACAGTCCCGCCGACCTGCTGCAGCACACCCTGCTGCGCTCCTACCGCGCCGACGAGTGGCCGCTGTGGTTCCAGGCGGCCGGACTGCCGGCGCACGCGCCACTGACCCGGAGCATCGTCTTCGACACCTCGCTGGCCATGCTCGAGGCGGCCCGCCAGGGTGTCGGCGTGGCCCTGGCGCCGGCGGCGATGTTTGCCCGGCAACTGGCCAGCGAGAGCATCCGGCGTCCGTTCGCCACCGAAGTGAGTACCGGCAGCTACTGGCTGACGCGCTTGCAGTCGCGGGGGGAGACCAGCGCGATGCTGGCGTTCCGGGGGTGGTTGCTGGAGATGGCTGCCGTTGAGGCGCGGGGGAGATAA", "fmax": "4593880", "accession": "AE004091.2", "fmin": "4592989", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "P24734.3", "sequence": "MVRPHLPLNALRAFEASARHLSFTRAAIELCVTQAAVSHQVKSLEERLGVALFKRLPRGLMLTHEGESLLPVLCDSFDRIAGLLERFEGGHYRDVLTVGAVGTFTVGWLLPRLEDFQARHPFIDLRLSTHNNRVDIAAEGLDYAIRFGGGAWHGTEALALFEAPLTVLCCPEVAAQLHSPADLLQHTLLRSYRADEWPLWFQAAGLPAHAPLTRSIVFDTSLAMLEAARQGVGVALAPAAMFARQLASESIRRPFATEVSTGSYWLTRLQSRGETSAMLAFRGWLLEMAAVEARGR"}}}}, "model_name": "Pseudomonas aeruginosa ampR with mutation conferring resistance to aztreonam", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36689": {"category_aro_name": "aztreonam", "category_aro_cvterm_id": "36689", "category_aro_accession": "3000550", "category_aro_class_name": "Antibiotic", "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."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "36029": {"category_aro_name": "IMP beta-lactamase", "category_aro_cvterm_id": "36029", "category_aro_accession": "3000020", "category_aro_class_name": "AMR Gene Family", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "36237": {"category_aro_name": "PDC beta-lactamase", "category_aro_cvterm_id": "36237", "category_aro_accession": "3000098", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa."}, "35923": {"category_aro_name": "monobactam", "category_aro_cvterm_id": "35923", "category_aro_accession": "0000004", "category_aro_class_name": "Drug Class", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "41396": {"category_aro_name": "ampC-type beta-lactamase", "category_aro_cvterm_id": "41396", "category_aro_accession": "3004232", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "Pseudomonas aeruginosa ampR with mutation conferring resistance to aztreonam", "model_type": "protein variant model", "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.", "CARD_short_name": "Paer_ampR_ATM", "ARO_id": "46259", "model_type_id": "40293"}, "5962": {"model_id": "5962", "ARO_accession": "3007492", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "A novel tetA-type efflux pump.", "model_sequences": {"sequence": {"8684": {"dna_sequence": {"partial": "0", "sequence": "ATGTCCATTTCCTTATCATTGATAAATTATGGTGAAGCTATGCAGACGGAAGCACGGATCAATAAATCTCTGGCCATTGTGCTCAGTGTCATTGTGCTGGATGCAATGGGGCTCGGGCTTGTGATGCCGGTTCTGCCGGAGTTGTTGCGCGGACTGGTGCCAGGCGGACAGGTAACAGGGCATTATGGTATGTTGCTGGCTGTCTATGCGCTGATGCAGGTGTTCTTTGCGCCGCTGCTAGGGCGATTGTCAGATCGCTATGGCCGCCGTCCGGTGCTGATTATGTCGCTTGCCGGTGCAGCAATTGACTATGCCGTCATGGCAGCAGCACCGGTGCTCTGGGTGATTTATATCGGCCGCATGATTGCCGGTATTACCGGAGCGACAGGTGCGGTTGCGGCATCGGCGATTGCCGATACGATGCCGTCAAACCAGCGGGCGCGCTGGTTCGGTTATATGGGCGCCTGTTACGGTGCCGGAATGATTGCGGGGCCTGCGATCGGCGGGCTGGCAGGCAGCCTGTCTGTGCACGCCCCCTTTATCGCGGCTGCTGTACTGAACGGAACCGGTTTTCTGCTGGCTTATCTTTTTCTCAAAGAGACACGTCCGGCAGGTTCGCAGCCGGCAGTTTCAGAAACATTCAGTTTGCGTGAGTTTCTGTTGCCGGTCAGCTTTCTCAAAGGGATGACCGCACTTGCGCTGGTGTTTTTCATTATCCAGCTGGTGGGGCAGCTTCCTGCAACATTGTGGGTGATCTATACGGAAGATCGTTTCGCGTGGGACACAACCATGGTCGGCTTTTCACTGGCGGCTTTCGGTGCCGTGCATACCGTGTTTCAGGCTTTTGTGACCGGCCCGCTCTCAGCCCGTTTTGGTGAGCGCCGCACATTGATCATCGGCATGGCTGCCGATGCCTGCGGTTTTCTGGCGCTGGCCATGATCACGCAAAGCTGGATGATACTGCCGGTACTATTGCTGCTGGCAACCGGCGGTGTCGGCATGCCCGCATTGCAGGCAATGTTGTCTGGGGCTGCCGGAGAGGATGAGCAGGGGAGTTTGCAGGGCACACTGACCAGCCTGACGAACCTGAGTTCGATTATCGGGCCCCTTGGTTTCTCGGCTTTCTACGCAATAACCGCAGTTGCATGGAATGGCTGGGTGTGGATTGGCGGTGCTGCGCTTTATTGCATCAGCTTCGCGATCCTGCGCCGGTCTTCATAA", "fmax": "33527", "accession": "MN340018.1", "fmin": "32306", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "QIQ10744.1", "sequence": "MSISLSLINYGEAMQTEARINKSLAIVLSVIVLDAMGLGLVMPVLPELLRGLVPGGQVTGHYGMLLAVYALMQVFFAPLLGRLSDRYGRRPVLIMSLAGAAIDYAVMAAAPVLWVIYIGRMIAGITGATGAVAASAIADTMPSNQRARWFGYMGACYGAGMIAGPAIGGLAGSLSVHAPFIAAAVLNGTGFLLAYLFLKETRPAGSQPAVSETFSLREFLLPVSFLKGMTALALVFFIIQLVGQLPATLWVIYTEDRFAWDTTMVGFSLAAFGAVHTVFQAFVTGPLSARFGERRTLIIGMAADACGFLALAMITQSWMILPVLLLLATGGVGMPALQAMLSGAAGEDEQGSLQGTLTSLTNLSSIIGPLGFSAFYAITAVAWNGWVWIGGAALYCISFAILRRSS"}}}}, "model_name": "tet(62)", "ARO_category": {"36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "36003": {"category_aro_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "category_aro_cvterm_id": "36003", "category_aro_accession": "0010002", "category_aro_class_name": "AMR Gene Family", "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."}, "35968": {"category_aro_name": "tetracycline", "category_aro_cvterm_id": "35968", "category_aro_accession": "0000051", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome."}, "36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}}, "ARO_name": "tet(62)", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "tet(62)", "ARO_id": "46260", "model_type_id": "40292"}, "5963": {"model_id": "5963", "ARO_accession": "3007493", "model_param": {"blastp_bit_score": {"param_value": "800", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "A tetracycline efflux MFS Transporter from Staphylococcus aureus.", "model_sequences": {"sequence": {"8685": {"dna_sequence": {"partial": "0", "sequence": "TTGAACTATATAAACAATAAAATTAAAAGCTTAAGTTATAATATTTTATTTTGGCTCTGTATTCTTTCATTTTTTAGCGTATTAAATGAAATGGTTTTAAACGTTTCACTTCCTGATATAGCTATTTCTTTTAATACTTCACCTGCTATTACTAATTGGGTTAATACTGCCTACATGCTAACTTTTTCAATTGGTACAGCAGTATACGGCAAATTATCTGATCAAGTAAGCATTAAAAAACTACTTATTTTAGGGATTATTTTAAGTTGCTTAGGCTCATTAATTGGATTTTTTGGTCATAAACATTTTTTAATTTTAATTTTAGGTAGGTTAATACAAGGAATAGGTTCTGCTGCGTTTCCTTCTCTTGTTATGGTTGTCGTATCACGTAATATAACTAAAGCAAAACAAGGGAAGGCATTTGGATTTATAGGATCAATTGTTGCATTGGGTGAAGGAATAGGGCCTTCAATAGGAGGCGTTGTAACTCATTATATTCATTGGTCATATTTACTTATAATACCTATTTTCACATTAATAACCATTCCTTTTCTTAATAAAATCATGGAACCTGGCGAATCTCAAAAAGGAGATTTAGATATATTAGGGATCCTTTTAATGTCTATAAGTATCATAAGCTTTATGTTATTTACAACAAGTTACAAATGGTTTTATTTAATAACCTTTGTTATTTTCTTTATCATTTTTATTAAACATATTGTAAAAGTTACCCATCCTTTTATTGACCCAGCTTTGCGGAAGAACCCATCATTTATTTTTGGATTGATTTCAGGAGCTCTTATATTTGCTACTGTAGCCGGATTTATCTCAATGGTTCCTTATATGATGAAAGCTCTTTACCATATAAACGCCGCGACAATTGGGAACAATGTTATTCTTCCTGGTACTATAAGTGTTATTATATTTGGATATATTGGTGGATACTTAGTAGATAAAAAAGGTGCTTTGTTTGTCTTTGTTATAGGTTCGCTATTTATATCTATTAGTTTTCTTGTTATTGCATTTTTTGTTGAATTAAATTTGTGGGTAACAACCATCTCTTTCATTTTTGTCATGGGAGGACTTTCATTTACAAAAACTGTTATATCAACGATAGTTTCTAGTAGCCTTTCTCATGAAGAAGTCGGTTCTGGTATGAGCTTATTAAATTTTACTAGTTTTTTATCAGAAGGCACAGGCATTATAATAATGGGCGGATTACTATCAACACAATTTTTAAATTATAATTTCCTTTCAGAATTCATTACTTTTTCCACCAACCTTTACAGTAATATCCTTATTGGTTGTACAATTATAATTGCACTTTGTTGTTTGTTAACATTTATATTATTTAATCGTACAGTAAAACAACACACTTAA", "fmax": "18024", "accession": "CP053076.1", "fmin": "16644", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus aureus", "NCBI_taxonomy_id": "1280", "NCBI_taxonomy_cvterm_id": "35508"}, "protein_sequence": {"accession": "QJR33972.1", "sequence": "MNYINNKIKSLSYNILFWLCILSFFSVLNEMVLNVSLPDIAISFNTSPAITNWVNTAYMLTFSIGTAVYGKLSDQVSIKKLLILGIILSCLGSLIGFFGHKHFLILILGRLIQGIGSAAFPSLVMVVVSRNITKAKQGKAFGFIGSIVALGEGIGPSIGGVVTHYIHWSYLLIIPIFTLITIPFLNKIMEPGESQKGDLDILGILLMSISIISFMLFTTSYKWFYLITFVIFFIIFIKHIVKVTHPFIDPALRKNPSFIFGLISGALIFATVAGFISMVPYMMKALYHINAATIGNNVILPGTISVIIFGYIGGYLVDKKGALFVFVIGSLFISISFLVIAFFVELNLWVTTISFIFVMGGLSFTKTVISTIVSSSLSHEEVGSGMSLLNFTSFLSEGTGIIIMGGLLSTQFLNYNFLSEFITFSTNLYSNILIGCTIIIALCCLLTFILFNRTVKQHT"}}}}, "model_name": "tet(63)", "ARO_category": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36003": {"category_aro_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "category_aro_cvterm_id": "36003", "category_aro_accession": "0010002", "category_aro_class_name": "AMR Gene Family", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35968": {"category_aro_name": "tetracycline", "category_aro_cvterm_id": "35968", "category_aro_accession": "0000051", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35986": {"category_aro_name": "doxycycline", "category_aro_cvterm_id": "35986", "category_aro_accession": "0000069", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "tet(63)", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "tet(63)", "ARO_id": "46261", "model_type_id": "40292"}, "5964": {"model_id": "5964", "ARO_accession": "3007494", "model_param": {"blastp_bit_score": {"param_value": "675", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "A tetracycline efflux MFS Transporter from Burkholderia ubonensis.", "model_sequences": {"sequence": {"8686": {"dna_sequence": {"partial": "0", "sequence": "TTGAATCCTTCCATGATTGCCATCCTGACGACCGTCGTGCTTGACGCGATCGGCGTCGGGCTCGTGATGCCGATCCTGCCCGGGCTGCTGCGCACCCTCGCCGGCGCGGGCGGCGCCGACACGCACTACGGCATGCTGCTCGCGCTGTACGCGCTGGCGCAGTTCCTGTGCGCCCCCGTCCTTGGCGCGCTGAGCGACCGCTTCGGCCGCCGGCCCGTGCTGCTCGCGTCGCTCGCGGGCGCCGCGCTCGACTACCTGCTGATGGCGTATGCGCCGACGCTCGCGTGGCTCTATGCCGGGCGGCTGATCGCGGGCATCACGGGCGCGAACGTCGCGGTCGCGACCGCGTACGTCACCGACGTGACCGCGGAACCCGATCGCGCGCGCCGTTTCGGTCAATTGGGCGCCGCGATGGGGATCGGCTTCATCGCCGGCCCGGTGCTCGGCGGCCTGCTCGGCGCGTGGCATCTGCGCGCGCCGTTCGCCGCCGCGGCGCTGCTCAATGCGCTCAATCTCGCACTCGTCTGGCGGAGCCTGCCGGAATCGCGGCCGCCGGCCGCGCGCGCCGGCCGCGCCACGGTGAGCCTCAACGCGTTCGCGAGCCTGCGGCGGCTGCGCGGCGGCCCGGCGCTCGTCCCGCTGATCGGCGTCTACGTGATCGTGGCGCTGGTGTCGCAGGCGCCCGCGACGCTGTGGATCCTGTACGGACAGGCGCATTTCGGCTGGTCGACGCCGGTCGCGGGCCTGTCGCTCGCCGGCTACGGCGCGTGCCACGCGCTCGCGCAGGCGTTCGCGATCGGGCCGCTGATCGCGCGGCTCGGTGAGCGTCGCGCGCTCGCGCTGGGCCTCGCCGGCGACGCGCTCGGCCTCGTGGTCATCGCGTTCGCCAACGCGGCCTGGGTGCCGTTCGCGCTATTGCCGCTGTTCGCGGCGGGCGGCATGACGCTGCCGGCGCTGCAGGCGATGCTCGCGCGCCAGGTCGACGATGCCCGGCAGGGCGAGCTGCAGGGCACGCTCGCGAGCGTCGCGAGCCTGATCGGCGTCGCCGGGCCGCTCGTCGTCACCGCGGCCTATGCGGCAACCCGCGACGCGTGGCCCGGGCTCGTCTGGGCCGCGGCCGCGTTGCTCTACCTGCTGGTGCCGCCGCTGCTGGCCCACGCGCGGCCGGCGCGAGAAAGTCCGGCCGCGTAA", "fmax": "1291", "accession": "NG_071182.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Burkholderia ubonensis", "NCBI_taxonomy_id": "101571", "NCBI_taxonomy_cvterm_id": "46263"}, "protein_sequence": {"accession": "WP_124470450.1", "sequence": "MNPSMIAILTTVVLDAIGVGLVMPILPGLLRTLAGAGGADTHYGMLLALYALAQFLCAPVLGALSDRFGRRPVLLASLAGAALDYLLMAYAPTLAWLYAGRLIAGITGANVAVATAYVTDVTAEPDRARRFGQLGAAMGIGFIAGPVLGGLLGAWHLRAPFAAAALLNALNLALVWRSLPESRPPAARAGRATVSLNAFASLRRLRGGPALVPLIGVYVIVALVSQAPATLWILYGQAHFGWSTPVAGLSLAGYGACHALAQAFAIGPLIARLGERRALALGLAGDALGLVVIAFANAAWVPFALLPLFAAGGMTLPALQAMLARQVDDARQGELQGTLASVASLIGVAGPLVVTAAYAATRDAWPGLVWAAAALLYLLVPPLLAHARPARESPAA"}}}}, "model_name": "tet(64)", "ARO_category": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36003": {"category_aro_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "category_aro_cvterm_id": "36003", "category_aro_accession": "0010002", "category_aro_class_name": "AMR Gene Family", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35968": {"category_aro_name": "tetracycline", "category_aro_cvterm_id": "35968", "category_aro_accession": "0000051", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35986": {"category_aro_name": "doxycycline", "category_aro_cvterm_id": "35986", "category_aro_accession": "0000069", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "tet(64)", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "tet(64)", "ARO_id": "46262", "model_type_id": "40292"}, "5965": {"model_id": "5965", "ARO_accession": "3007509", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "AcrA is a subunit of the AcrAB multidrug efflux system found in Shigella flexneri, which is encoded by the acrRAB operon.", "model_sequences": {"sequence": {"8687": {"dna_sequence": {"partial": "0", "sequence": "ATGAACAAAAACAGAGGGTTTACGCCTCTGGCGGTCGTTCTGATGCTCTCAGGCAGCTTAGCCCTAACAGGATGTGACGACAAACAGGCCCAACAAGGTGGCCAGCAGATGCCCGCCGTTGGCGTAGTAACAGTCAAAACTGAACCTCTGCAGATCACAACCGAGCTTCCAGGTCGCACCAGTGCCTACCGGATCGCAGAAGTTCGTCCTCAAGTTAGCGGGATTATCCTGAAGCGTAATTTCAAAGAAGGTAGCGACATCGAAGCTGGTGTCTCTCTCTATCAGATTGATCCTGCGACCTATCAGGCGACATACGACAGTGCGAAAGGTGATCTGGCGAAAGCCCAGGCTGCAGCCAATATCGCGCAATTGACGGTGAATCGTTATCAGAAACTGCTCGGTACTCAGTACATCAGTAAGCAAGGGTACGATCAGGCTCTGGCTGATGCGCAACAGGCGAATGCTGCGGTAACTGCGGCGAAAGCTGCCGTTGAAACTGCGCGGATCAATCTGGCTTACACCAAAGTCACCTCTCCGATTAGCGGTCGCATTGGTAAGTCGAACGTGACGGAAGGCGCATTGGTACAGAACGGTCAGGCGACTGTGCTGGCAACCGTGCAGCAACTTGATCCGATCTACGTTGATGTGACCCAGTCCAGCAACGACTTCCTTCGCCTGAAACAGGAACTGGCGAATGGCACGCTGAAACAAGAGAACGGCAAAGCCAAAGTGTCGCTGATCACCAGTGACGGCATTAAGTTCCCGCAGGACGGTACGCTGGAATTCTCTGACGTTACCGTTGATCAGACCACTGGGTCTATCACCCTACGCGCTATCTTCCCGAACCCGGATCACACTCTGCTGCCGGGTATGTTCGTGCGCGCACGTCTGGAAGAAGGGCTTAATCCAAACGCTATTTTAGTCCCGCAACAGGGCGTAACCCGTACGCCGCGTGGTGATGCCACCGTACTGGTAGTTGGCGCGGATGACAAAGTGGAAACCCGTCCGATCGTTGCAAGCCAGGCTATTGGCGATAAGTGGCTGGTGACAGAAGGTCTGAAAGCAGGCGATCGCGTAGTAATAAGTGGGCTGCAGAAAGTGCGTCCTGGTGTCCAGGTAAAAGCACAAGAAGTTACCGCTGATAATAACCAGCAAGCCGCAAGCGGTGCTCAGCCTGAACAGTCCAAGTCTTAA", "fmax": "422150", "accession": "NC_004337.2", "fmin": "420956", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shigella flexneri 2a str. 301", "NCBI_taxonomy_id": "198214", "NCBI_taxonomy_cvterm_id": "40665"}, "protein_sequence": {"accession": "NP_706356.2", "sequence": "MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQGYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATVLATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS"}}}}, "model_name": "Shigella flexneri acrA", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "37250": {"category_aro_name": "triclosan", "category_aro_cvterm_id": "37250", "category_aro_accession": "3000870", "category_aro_class_name": "Antibiotic", "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)."}, "36308": {"category_aro_name": "rifampin", "category_aro_cvterm_id": "36308", "category_aro_accession": "3000169", "category_aro_class_name": "Antibiotic", "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."}, "36005": {"category_aro_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "category_aro_cvterm_id": "36005", "category_aro_accession": "0010004", "category_aro_class_name": "AMR Gene Family", "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."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "36526": {"category_aro_name": "phenicol antibiotic", "category_aro_cvterm_id": "36526", "category_aro_accession": "3000387", "category_aro_class_name": "Drug Class", "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."}, "36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_class_name": "Efflux Component", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35949": {"category_aro_name": "tigecycline", "category_aro_cvterm_id": "35949", "category_aro_accession": "0000030", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome."}, "35960": {"category_aro_name": "glycylcycline", "category_aro_cvterm_id": "35960", "category_aro_accession": "0000042", "category_aro_class_name": "Drug Class", "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."}, "35954": {"category_aro_name": "ciprofloxacin", "category_aro_cvterm_id": "35954", "category_aro_accession": "0000036", "category_aro_class_name": "Antibiotic", "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."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "36524": {"category_aro_name": "chloramphenicol", "category_aro_cvterm_id": "36524", "category_aro_accession": "3000385", "category_aro_class_name": "Antibiotic", "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."}, "43746": {"category_aro_name": "disinfecting agents and antiseptics", "category_aro_cvterm_id": "43746", "category_aro_accession": "3005386", "category_aro_class_name": "Drug Class", "category_aro_description": "Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance."}, "35968": {"category_aro_name": "tetracycline", "category_aro_cvterm_id": "35968", "category_aro_accession": "0000051", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome."}, "36296": {"category_aro_name": "rifamycin antibiotic", "category_aro_cvterm_id": "36296", "category_aro_accession": "3000157", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "Shigella flexneri acrA", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Sfle_acrA", "ARO_id": "46278", "model_type_id": "40292"}, "5966": {"model_id": "5966", "ARO_accession": "3007510", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "dfrv is a plasmid-encoded dihydrofolate reductase found in Shigella sonnei.", "model_sequences": {"sequence": {"8740": {"dna_sequence": {"partial": "0", "sequence": "ATGGCTGCAAAAGCGAAAAACGGAGTGATTGGTTGCGGTCCACACATACCCTGGTCCGCGAAAGGAGAGCAGCTACTCTTTAAAGCCTTGACGTACAACCAGTGGCTTTTGGTGGGCCGCAAGACGTTCGAATCTATGGGAGCACTCCCTAATAGGAAATACGCGGTCGTTACTCGCTCAGCCTGGACGGCCGATAATGACAACGTAATAGTATTCCCGTCGATCGAAGAGGCCATGTACGGGCTGGCTGAACTCACCGATCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACATTGCCCATGGCCTCTACGCTCCCATATATCGACGATTGA", "fmax": "451", "accession": "KX777251.1", "fmin": "109", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shigella sonnei", "NCBI_taxonomy_id": "624", "NCBI_taxonomy_cvterm_id": "36790"}, "protein_sequence": {"accession": "AOY10467.1", "sequence": "MAAKAKNGVIGCGPHIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSAWTADNDNVIVFPSIEEAMYGLAELTDHVIVSGGGEIYRETLPMASTLPYIDD"}}}}, "model_name": "dfrv", "ARO_category": {"36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "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."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "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."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "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."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}}, "ARO_name": "dfrv", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "dfrv", "ARO_id": "46279", "model_type_id": "40292"}, "5967": {"model_id": "5967", "ARO_accession": "3007515", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "ANT(9)-Ic encodes an intrinsic, chromosomal aminoglycoside nucleotidyltransferase in Brucella intermedia.", "model_sequences": {"sequence": {"8689": {"dna_sequence": {"partial": "0", "sequence": "ATGGATAGAAATCACGCAGCAATCCCCGAAGAAGCGGCAAAGGCCCTGATCGTCCTGCAGGAATGCCTGGGGTCATCCTTGCAGGCCCTATATCTGCATGGCTCCGCCGTGAATGGCGGCCTTCGCCCCAACAGCGACGTCGACCTGCTGGCGGTCTGTGACCGGAATCCGGCACCTGAAACCAGTGCGCTTCTCGTTGATCGGCTGATGCAGATATCGGGCCGGCACCCGGTCGCCCCGGGAATGCCCCGATGCCTGGAGGTGATGCTCTTTCTGCGGCAGGACCTCGCCGCATCTCGCTATCCTGCGCGGTGCGCCTTCATCTATGGAGAATGGCTGCGTGACGAATTCGAGGCCGGGATCGTGCCGCAGGCCCATACCGACCCTGAATATACACTGGTGCTCGCGCAAGCCGGCCAAGAAGCAATAAGCCTTGTCGGCCCCACGCGGGAGCATCTTCTGCCGTCCGTGCCGCAAGGAGACGTGCGACGGGCGATTGCCGATGCCTTGCCTGCCCTTATCGGCAACCTTGCAGGCGATGAGCGCAATGTCCTGCTGACGCTGGCGCGGATGTGGTACACGCTCGAAACCGGAACATTCGTGCCGAAGGACGCCGCCGCCGAATGGGCGCTGCCCCTTGTTTCCCCCGAAACCGCAGCAGCCCTTGCGCTCGCGCAGGCGGCCTATCGGGGCGCGGCTGTCGACGACTGGCAAAGCCATCCCCTGCTCGCAGGGCAGGCGGCTGAGGAACTGGCACATCAGGTGCGGCTGCTTTTCTGA", "fmax": "1047", "accession": "MZ241296.1", "fmin": "267", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brucella intermedia", "NCBI_taxonomy_id": "94625", "NCBI_taxonomy_cvterm_id": "45773"}, "protein_sequence": {"accession": "QWQ57435.1", "sequence": "MDRNHAAIPEEAAKALIVLQECLGSSLQALYLHGSAVNGGLRPNSDVDLLAVCDRNPAPETSALLVDRLMQISGRHPVAPGMPRCLEVMLFLRQDLAASRYPARCAFIYGEWLRDEFEAGIVPQAHTDPEYTLVLAQAGQEAISLVGPTREHLLPSVPQGDVRRAIADALPALIGNLAGDERNVLLTLARMWYTLETGTFVPKDAAAEWALPLVSPETAAALALAQAAYRGAAVDDWQSHPLLAGQAAEELAHQVRLLF"}}}}, "model_name": "ANT(9)-Ic", "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35957": {"category_aro_name": "spectinomycin", "category_aro_cvterm_id": "35957", "category_aro_accession": "0000039", "category_aro_class_name": "Antibiotic", "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."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}, "36367": {"category_aro_name": "ANT(9)", "category_aro_cvterm_id": "36367", "category_aro_accession": "3000228", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "ANT(9)-Ic", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "ANT(9)-Ic", "ARO_id": "46284", "model_type_id": "40292"}, "6004": {"model_id": "6004", "ARO_accession": "3007674", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13141": "T33A"}, "clinical": {"13141": "T33A"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "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.", "model_sequences": {"sequence": {"8727": {"dna_sequence": {"partial": "0", "sequence": "GTGAGCGTCAACGACGGGGTCGATCAGATGGGCGCCGAGCCCGACATCATGGAATTCGTCGAACAGATGGGCGGCTATTTCGAGTCCAGGAGTTTGACTCGGTTGGCGGGTCGATTGTTGGGCTGGCTGCTGGTGTGTGATCCCGAGCGGCAGTCCTCGGAGGAACTGGCGACGGCGCTGGCGGCCAGCAGCGGGGGGATCAGCACCAATGCCCGGATGCTGATCCAATTTGGGTTCATTGAGCGGCTCGCGGTCGCCGGGGATCGGCGCACCTATTTCCGGTTGCGGCCCAACGCTTTCGCGGCTGGCGAGCGTGAACGCATCCGGGCAATGGCCGAACTGCAGGACCTGGCTGACGTGGGGCTGAGGGCGCTGGGCGACGCCCCGCCGCAGCGAAGCCGACGGCTGCGGGAGATGCGGGATCTGTTGGCATATATGGAGAACGTCGTCTCCGACGCCCTGGGGCGATACAGCCAGCGAACCGGAGAGGACGACTGA", "fmax": "779487", "accession": "NC_000962.3", "fmin": "778989", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "NP_215192.1", "sequence": "MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD"}}}}, "model_name": "Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to bedaquiline", "ARO_category": {"46454": {"category_aro_name": "bedaquiline resistant Rv0678", "category_aro_cvterm_id": "46454", "category_aro_accession": "3007673", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Loss-of-function mutations in rv0678 are a common mechanism of resistance."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "41932": {"category_aro_name": "diarylquinoline antibiotic", "category_aro_cvterm_id": "41932", "category_aro_accession": "3004491", "category_aro_class_name": "Drug Class", "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."}, "41933": {"category_aro_name": "bedaquiline", "category_aro_cvterm_id": "41933", "category_aro_accession": "3004492", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to bedaquiline", "model_type": "protein variant model", "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.", "CARD_short_name": "Mtub_Rv0678_BDQ", "ARO_id": "46455", "model_type_id": "40293"}, "6005": {"model_id": "6005", "ARO_accession": "3007678", "model_param": {"blastp_bit_score": {"param_value": "1400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8733": {"dna_sequence": {"partial": "0", "sequence": "ATGATAGAAATCGGCAAGAAGCTGAATGGTCGATATCACATTATTGGCAGCATCGGAAGCGGCGGCATGGCCAACGTCTATTTAGCACACGATTTAATTTTAGACCGAGACGTTGCAGTAAAAGTCTTGCGCTTTGACTTCCAAAACGATCAAGCCGCCATCCGACGTTTTCAGCGTGAAGCACTAGCCGCAACTGAGCTGGTTCACCCGAATATCGTCAGTGTGTACGATGTAGGCGAAGAAGATGGACTACAATATTTAGTCATGGAATATGTGAAAGGAATGGACTTGAAACGTTACATCCAAACGCATTTCCCAATTACTTATTCCACAGTTGTGGATATTACGCAACAAATTTTATCTGCTGTCGCAATGGCACATGAACATAGAATTATTCACCGGGATTTAAAACCGCAAAACATTCTGATTGACGAACACGGCACAGTCAAAATTACTGACTTTGGGATTGCGATTGCTTTGTCAGAAACGTCAATTACGCAAACGAACACAATGTTAGGTTCGGTGCATTACTTATCGCCAGAACAAGCGCGCGGAAGCATGGCGACTAACCAATCAGATATTTACGCTGTGGGAATTATTCTCTATGAAATGCTAACAGGGAATGTACCTTTTGATGGTGAATCAGCCGTAACGATTGCCTTAAAACATTTTCAAGAAGAAATTCCTTCTGTCAAAATGTTTGATCCAGGGATTCCTCAATCATTGGAAAATGTGGTTCGTCATGCAACCGCAAAAGACCCAAGCGATCGCTACAAAACAGCGAATGAGATGGCAGAAGACTTATACACGTCCTTGTCAGCCAGTCGTTTAAACGAACCTGCGTGGGAACCAACGGCTTTATTAGGAGAAACGAAAGTATTAACTCCGATTCCCGAAGACATCGCTGAACCGGAAGAGACAACGCCTGTCGAAGTCCCAGAAGATATCGCAGATGACATTTTAGCTGAACAACCACCGAAGAAAAACCGTAAAAAATTGTGGATTGGCTTAGCAATTGCGGCATTAATTGCTTTAGCAATAGGTGGCTTAGCCTTTGCAATGTCGGGTGGTAAAGACGTTGAAGTTCCTGATGTTACAAACGAAACGAAAGCGGACGCTTCACAAGCGCTACAAAGTGCCGGGCTGAAAGTCGATAGTGAAACCAAAAAAATTCCCGATGATAAGATTGAAGAAGGCAAGGTGGTCAAAACAGACCCCGAAGCAAAATCATCTGTGAAAAAAGGCCGATCTGTTACTTTATACATCAGCTCTGGAACAGAAAAAATTGAGATGGCCGATTATACAAATGAATCGTATGAATCTGCTGTCGAAGCCTTGAAAAAACTAGGGTTTTCAGAAGATCAAATTACAACGAAAAAAGAATACAGTGATTCTGTGTCTACGGATAGCATTATTAAACAAAAACCAGCTGCAGGTAAAAAAGTTGATCCGAAAAAAGACAAAGTCACTTTAACGGTCAGTGAAGGACCAGAAGCGGTTACTTTGCCTAGTTACGCCGGTTATTCTTACGAAAATGCAGTAATTGCACTGAAACAATTAGGCATTTCTGACTCTCAAATTACGCGTGTCGACCAAGCAAGCGATACGGTAGAACCAGGTTTAGTCATTACGCAAGACCCCGCACCAGGTGGGACCGTGACACCTAAAAATGGCCAAGTGACGTTATATGTAAGTAAAGGTAGCGACAAAGTGACACTTTCTGATTATAGCGGAATTTCTTACGATAATGCGGTAAGTCGCTTAATTGCTTTAGGTATCCCAGAATCTCAAATTAAACGAGTGGACGAAGAAAGCGACAAAGTTGAAAAAGATACCGTGATTAGTCAAGAACCAGCTTCTGGTACCGCTGTTGATCCGAAAAATGACACGATTACTTTACATGTCAGCAAAGGCAGTGACTCAGTAACTGTTCCTGATATTTCAGGTTATTCGCCAAAAGCTGCAGAAGACAGCATCAATAATGCTGGCCTTAAAATCAATGAACAAGGATTATCTGGCTCTGGCGATGGCCAAGTCGTTGAACGAACTAGCCCATCCGCTGGCAGCAAAGTCAAAAAAGGCGACGCTGTTACGGTTTATTATTCAAAAGCAAATGATTCAAAAAGCACCACTAGTGAAAGTAGTACGAGTAATTAA", "fmax": "2494361", "accession": "CP124778.1", "fmin": "2492204", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterococcus faecalis", "NCBI_taxonomy_id": "1351", "NCBI_taxonomy_cvterm_id": "35918"}, "protein_sequence": {"accession": "WKR28567.1", "sequence": "MIEIGKKLNGRYHIIGSIGSGGMANVYLAHDLILDRDVAVKVLRFDFQNDQAAIRRFQREALAATELVHPNIVSVYDVGEEDGLQYLVMEYVKGMDLKRYIQTHFPITYSTVVDITQQILSAVAMAHEHRIIHRDLKPQNILIDEHGTVKITDFGIAIALSETSITQTNTMLGSVHYLSPEQARGSMATNQSDIYAVGIILYEMLTGNVPFDGESAVTIALKHFQEEIPSVKMFDPGIPQSLENVVRHATAKDPSDRYKTANEMAEDLYTSLSASRLNEPAWEPTALLGETKVLTPIPEDIAEPEETTPVEVPEDIADDILAEQPPKKNRKKLWIGLAIAALIALAIGGLAFAMSGGKDVEVPDVTNETKADASQALQSAGLKVDSETKKIPDDKIEEGKVVKTDPEAKSSVKKGRSVTLYISSGTEKIEMADYTNESYESAVEALKKLGFSEDQITTKKEYSDSVSTDSIIKQKPAAGKKVDPKKDKVTLTVSEGPEAVTLPSYAGYSYENAVIALKQLGISDSQITRVDQASDTVEPGLVITQDPAPGGTVTPKNGQVTLYVSKGSDKVTLSDYSGISYDNAVSRLIALGIPESQIKRVDEESDKVEKDTVISQEPASGTAVDPKNDTITLHVSKGSDSVTVPDISGYSPKAAEDSINNAGLKINEQGLSGSGDGQVVERTSPSAGSKVKKGDAVTVYYSKANDSKSTTSESSTSN"}}}}, "model_name": "IreK", "ARO_category": {"36383": {"category_aro_name": "reduced permeability to antibiotic", "category_aro_cvterm_id": "36383", "category_aro_accession": "3000244", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance."}, "46469": {"category_aro_name": "Serine/threonine kinases", "category_aro_cvterm_id": "46469", "category_aro_accession": "3007683", "category_aro_class_name": "AMR Gene Family", "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."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35979": {"category_aro_name": "ceftriaxone", "category_aro_cvterm_id": "35979", "category_aro_accession": "0000062", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "IreK", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "IreK", "ARO_id": "46460", "model_type_id": "40292"}, "6011": {"model_id": "6011", "ARO_accession": "3007682", "model_param": {"blastp_bit_score": {"param_value": "900", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "Mdtq is a putative multidrug resistance outer membrane protein found in carbapenem resistant Klebsiella pneumoniae.", "model_sequences": {"sequence": {"8739": {"dna_sequence": {"partial": "0", "sequence": "ATGAAATTGATATTAAATAAAAGCGTGCTGGCGGCATTGCCCCTGGCCATCGCGCTGGCTGGCTGCGCGCCATCTCATGAGGTTGCTAATCCGCCGCAGCAGCAAATTCCAGCCTCCCATGTTTCCATGGATCTCCCTGCCGCCGTGAAAAATGGCTGGCCGCAGACTGACTGGTGGAAAGATTACCATGACCCACAGCTTAATAATCTGATTCAGCGAGCGTTGGCCAACGCGCCGGATATGCAGATTGCCGAACAGCGCATCAGGCTTGCCGAAGCGCAGGCGCGAATGTCGCAGGCGAATCTTGGCCCGGAGATGGATTTCTCCGCCGATATTGAACGCCAGCGCATGTCGGCCGAAGGCCTGATGGGACCGTTTGCTACCGACACCGACGGCAATACCGGCCCGTGGTACACCAACGGTACCTTTGGCCTGACCGCCGGTTGGGATCTCGATCTGTGGGGAAAAAACCGTGCGCTGGTGAAAGCGCGTATCGGCGAGCTGAAAGCCCAGGTTGCTGAACAGGCCCAGACCCGTGAGCTGCTCTCCGGCAGCGTGGCGCGTCTGTACTGGCAGTGGCAGACGGAAGCGGCGATCAAAGCGGTGCTGCAGCAGGTGAAAAACGAGCAAAATAATATCGTGACGGTCGACAAGGCCCTGTATCAGCGCGGGATCACTAACTCCGCCGAAGGGGCGGAGAACGATATTAACGTCAGCAAAACCGACCAGCAGCTGGCGGACGTGACGGGCACGATGAAAGAGATTGAAGCGCGGCTGATGGCCCTGACCAACAGCCAGAGCCAGTCGCTAAACCTCAAACCCGCCAGCCTGCCAACGGTCAGCGCGCAGCTGCCAGATACCCTCGGCTATGAGCTGCTGGCGCGCCGCCCGGATCTGCAGGTCGCCCACTGGTATATTGAGGCGTCCCTGAGCGAAGTGGACGCGGCGAAAGCGGCGTTTTATCCGGACATCAATCTGATGGCGTTCCTGCAGCAGGATGCCCTGCACTTAAGCGATCTTTTCCGCCATTCGGCGCAGCAGATGGGCGTTACTGCCGGGTTGACGCTGCCGATCTTTGACAGCGGCCGCCTTAACGCCAACCTGGATATCGCCAGCGCGCAGAATAGCCTGTCGATCGCCCAGTACAACAAAGCGGTGGTGGATGCCGTTAACCAGGTGGCGAAAACCGCCAGCCAGGTCGAAACATTAATGGCCAAAAGCCAGCAGCAGCAGCAGGTTGAAAAAGACGCTCAACGGGTAGTAGATCTGGCGCAGGCCCGAATGGCGGCGGGGATCTTACCTGGCTCCAGAGTCAGTATGGCGAAGCTCCCGGCGCTGCAGGAGCGGATCACCGCATTGCGCCTGCACGGCCAGTGGATTGACGCTAGCATTCAACTGACCTCGGCCCTCGGCGGCGGCTACCACCAGACGGTGAAGTAA", "fmax": "5053037", "accession": "CP133868.1", "fmin": "5051597", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "WMY66391.1", "sequence": "MKLILNKSVLAALPLAIALAGCAPSHEVANPPQQQIPASHVSMDLPAAVKNGWPQTDWWKDYHDPQLNNLIQRALANAPDMQIAEQRIRLAEAQARMSQANLGPEMDFSADIERQRMSAEGLMGPFATDTDGNTGPWYTNGTFGLTAGWDLDLWGKNRALVKARIGELKAQVAEQAQTRELLSGSVARLYWQWQTEAAIKAVLQQVKNEQNNIVTVDKALYQRGITNSAEGAENDINVSKTDQQLADVTGTMKEIEARLMALTNSQSQSLNLKPASLPTVSAQLPDTLGYELLARRPDLQVAHWYIEASLSEVDAAKAAFYPDINLMAFLQQDALHLSDLFRHSAQQMGVTAGLTLPIFDSGRLNANLDIASAQNSLSIAQYNKAVVDAVNQVAKTASQVETLMAKSQQQQQVEKDAQRVVDLAQARMAAGILPGSRVSMAKLPALQERITALRLHGQWIDASIQLTSALGGGYHQTVK"}}}}, "model_name": "Mdtq", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "41442": {"category_aro_name": "Outer Membrane Porin (Opr)", "category_aro_cvterm_id": "41442", "category_aro_accession": "3004278", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "36383": {"category_aro_name": "reduced permeability to antibiotic", "category_aro_cvterm_id": "36383", "category_aro_accession": "3000244", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "35923": {"category_aro_name": "monobactam", "category_aro_cvterm_id": "35923", "category_aro_accession": "0000004", "category_aro_class_name": "Drug Class", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}}, "ARO_name": "Mdtq", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "Mdtq", "ARO_id": "46464", "model_type_id": "40292"}, "6010": {"model_id": "6010", "ARO_accession": "3001708", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "OXA-105 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"8738": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATATTTTACTTGCTATGTGTTTGCCTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGCTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGCGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA", "fmax": "58126", "accession": "JANRFO010000004.1", "fmin": "57304", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter radioresistens", "NCBI_taxonomy_id": "40216", "NCBI_taxonomy_cvterm_id": "39672"}, "protein_sequence": {"accession": "WP_265760908.1", "sequence": "MNKYFTCYVFASLFLSGCTVQHNLINETPSQIAQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQAGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"}}}}, "model_name": "OXA-105", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35973": {"category_aro_name": "oxacillin", "category_aro_cvterm_id": "35973", "category_aro_accession": "0000056", "category_aro_class_name": "Antibiotic", "category_aro_description": "Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis."}, "35930": {"category_aro_name": "cloxacillin", "category_aro_cvterm_id": "35930", "category_aro_accession": "0000011", "category_aro_class_name": "Antibiotic", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-105", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "OXA-105", "ARO_id": "38108", "model_type_id": "40292"}, "5957": {"model_id": "5957", "ARO_accession": "3007483", "model_param": {"blastp_bit_score": {"param_value": "475", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "RAD-1 is a class D RAD beta-lactamase found in Riemerella anatipestifer.", "model_sequences": {"sequence": {"8679": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAACAAAAATAGTAGGCACAGTTATTTTGATTTTTATAGAATTCATTAGTTGCCATCACAATAAGAGTAAAAATAATTGGAAGTCTTTTTTTAAAGATAATAATGTAAACGGGACATTTGTACTAAAAAAGTTAAATTCAAATGAAACTCTAATTTACAATCAAGAGAGAAGTGATAAAAAATATACACCTGCTTCCACCTTTAAAATTCTAAACTCTATGATTGCATTACAGGTATTGTCTGTTACAGATGTAAATGACACAATTCAATGGGACGGAATAGACCGAGGATATGAATCTTGGAATAAAGATCAAACCATGAAATCCGCATTGCCTATTTCATGTGTATGGTTTTACCAAGAATTGGCTCGTAGAACGGGACAAAAAGAAATGCAAAAATGGCTTACAAAATCAAACTATGGGAATAAGAAAATTGGGAGTAAAATTGACAAATTTTGGCTTGATGGTACTCTTGCTATTTCGGCAAATGAACAAATTGTTTTTCTTGAAAAACTCATAAATAATAAATTACCATTTGATAAAAACATTCAAGAGAGCGTAAAAAAAATAATGATTACAGACTCTACAGAACATTATATCATTCACTCAAAAACAGGCTGGGGAAACAATATAGGCTGGAATATAGGTTATATAGAAACAAAAAATAATATTTGGATTTTTGCATTGAATATGGATATGAATGACATAAAAATGGCAGATATAAGAAAAAAAATAACTTATAACATTTTAAAAGATCAAAAAATAATTCAATAG", "fmax": "214951", "accession": "CP104076.1", "fmin": "214174", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Riemerella anatipestifer", "NCBI_taxonomy_id": "34085", "NCBI_taxonomy_cvterm_id": "36951"}, "protein_sequence": {"accession": "UWS41116.1", "sequence": "MKTKIVGTVILIFIEFISCHHNKSKNNWKSFFKDNNVNGTFVLKKLNSNETLIYNQERSDKKYTPASTFKILNSMIALQVLSVTDVNDTIQWDGIDRGYESWNKDQTMKSALPISCVWFYQELARRTGQKEMQKWLTKSNYGNKKIGSKIDKFWLDGTLAISANEQIVFLEKLINNKLPFDKNIQESVKKIMITDSTEHYIIHSKTGWGNNIGWNIGYIETKNNIWIFALNMDMNDIKMADIRKKITYNILKDQKIIQ"}}}}, "model_name": "RAD-1", "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "46249": {"category_aro_name": "RAD beta-lactamase", "category_aro_cvterm_id": "46249", "category_aro_accession": "3007482", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "RAD beta-lactamases are a class D beta-lactamase first identified in Riemerella anatipestifer."}}, "ARO_name": "RAD-1", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "RAD-1", "ARO_id": "46250", "model_type_id": "40292"}, "5959": {"model_id": "5959", "ARO_accession": "3007490", "model_param": {"blastp_bit_score": {"param_value": "150", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8681": {"dna_sequence": {"partial": "0", "sequence": "ATGGATCAAAGTAGTAAAGAGGTTGGCACTCCCGTTGTTGGCCAGTTTGCACTCCCGTCGCACGCCACGTTTGGCCTTGGAGACCGCGTTCGCAAGAAATCGGGCGCCGCTTGGCAGGGTCAAGTTGTGGGCTGGTATTGCACAAAGCTGACCCCTGAAGGCTATGCCGTCGAGTCCGAGTCTCACCCAGGCTCGGTACAAATTTATCCAGTGAATGCGCTTGAACGCGTGGCCTGA", "fmax": "114376", "accession": "PHCQ01000010.1", "fmin": "114139", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Betaproteobacteria bacterium HGW-Betaproteobacteria-16", "NCBI_taxonomy_id": "2013707", "NCBI_taxonomy_cvterm_id": "46258"}, "protein_sequence": {"accession": "PKO69073.1", "sequence": "MDQSSKEVGTPVVGQFALPSHATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVNALERVA"}}}}, "model_name": "dfrB11", "ARO_category": {"36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "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."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "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."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "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."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}}, "ARO_name": "dfrB11", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "dfrB11", "ARO_id": "46257", "model_type_id": "40292"}, "5958": {"model_id": "5958", "ARO_accession": "3007489", "model_param": {"blastp_bit_score": {"param_value": "150", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "A dihydrofolate reductase and trimethoprim resistance gene found on a mega-plasmid (0.4 Mb) from a Pseudomonas putida strain.", "model_sequences": {"sequence": {"8680": {"dna_sequence": {"partial": "0", "sequence": "ATGGATCAAAGTAGCAATGAAGTCAGCACTCCAGTTGCTGGCCAGTTTGCGCTCCCATTGCGCGCCACGTTTGGCCTGGGAGATCGCGTACGCAAGAAATCTGGCGCCGCTTGGCAAGGTCAAGTTGTCGGCTGGTACTGCACAAAACTGACCCCTGAAGGCTATGCAGTCGAGTCCGAGTCTCACCCAGGCTCAGTACAGATTTATCCTGTGGCTGCGCTTGAACGCGTGGCCTAA", "fmax": "208414", "accession": "KU130294.1", "fmin": "208177", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas putida", "NCBI_taxonomy_id": "303", "NCBI_taxonomy_cvterm_id": "36803"}, "protein_sequence": {"accession": "ALZ46148.1", "sequence": "MDQSSNEVSTPVAGQFALPLRATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"}}}}, "model_name": "dfrB10", "ARO_category": {"36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "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."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "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."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "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."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}}, "ARO_name": "dfrB10", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "dfrB10", "ARO_id": "46256", "model_type_id": "40292"}, "5979": {"model_id": "5979", "ARO_accession": "3007632", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "FRI-11 is a FRI-type carbapenem-hydrolyzing class A beta-lactamase.", "model_sequences": {"sequence": {"8701": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTAAGAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTAGCTGCATCCGTATTAAAAAAAACTCAGGAGAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA", "fmax": "57369", "accession": "CP074152.1", "fmin": "56484", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter sp. JBIWA008", "NCBI_taxonomy_id": "2831892", "NCBI_taxonomy_cvterm_id": "46406"}, "protein_sequence": {"accession": "UAN43462.1", "sequence": "MFFLRKSASTFIFLLCLPLNSFASQESNSVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQEKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKNAAKIAINAVYGSYK"}}}}, "model_name": "FRI-11", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36309": {"category_aro_name": "imipenem", "category_aro_cvterm_id": "36309", "category_aro_accession": "3000170", "category_aro_class_name": "Antibiotic", "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."}, "42915": {"category_aro_name": "FRI beta-lactamase", "category_aro_cvterm_id": "42915", "category_aro_accession": "3004796", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35990": {"category_aro_name": "meropenem", "category_aro_cvterm_id": "35990", "category_aro_accession": "0000073", "category_aro_class_name": "Antibiotic", "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."}, "35987": {"category_aro_name": "ertapenem", "category_aro_cvterm_id": "35987", "category_aro_accession": "0000070", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis."}}, "ARO_name": "FRI-11", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "FRI-11", "ARO_id": "46405", "model_type_id": "40292"}, "5978": {"model_id": "5978", "ARO_accession": "3007562", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8700": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGATGGTGGTATTCGAATTTCGGCCACTGAGCAAATCACCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "798", "accession": "OK180618.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shewanella xiamenensis", "NCBI_taxonomy_id": "332186", "NCBI_taxonomy_cvterm_id": "39674"}, "protein_sequence": {"accession": "UBJ91324.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQITFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "model_name": "OXA-1039", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35973": {"category_aro_name": "oxacillin", "category_aro_cvterm_id": "35973", "category_aro_accession": "0000056", "category_aro_class_name": "Antibiotic", "category_aro_description": "Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis."}, "35930": {"category_aro_name": "cloxacillin", "category_aro_cvterm_id": "35930", "category_aro_accession": "0000011", "category_aro_class_name": "Antibiotic", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}, "35990": {"category_aro_name": "meropenem", "category_aro_cvterm_id": "35990", "category_aro_accession": "0000073", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "OXA-1039", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "OXA-1039", "ARO_id": "46335", "model_type_id": "40292"}, "5972": {"model_id": "5972", "ARO_accession": "3007536", "model_param": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "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)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13072": "A1401G", "13074": "G1484T", "13075": "C462T", "13076": "A514C", "13077": "C1402T"}, "clinical": {"13072": "A1401G", "13074": "G1484T", "13075": "C462T", "13076": "A514C", "13077": "C1402T"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "ARO_description": "Point mutation in M. tuberculosis rrnS conferring resistance to amikacin antibiotic.", "model_sequences": {"sequence": {"8695": {"dna_sequence": {"partial": "0", "sequence": "TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT", "fmax": "1473382", "accession": "NC_000962.3", "fmin": "1471845", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "model_name": "Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to amikacin", "ARO_category": {"35966": {"category_aro_name": "kanamycin A", "category_aro_cvterm_id": "35966", "category_aro_accession": "0000049", "category_aro_class_name": "Antibiotic", "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."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}, "40277": {"category_aro_name": "16s rRNA with mutation conferring resistance to aminoglycoside antibiotics", "category_aro_cvterm_id": "40277", "category_aro_accession": "3003666", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides."}}, "ARO_name": "Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to amikacin", "model_type": "rRNA gene variant model", "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.", "CARD_short_name": "Mtub_16rrnS_AMK", "ARO_id": "46307", "model_type_id": "40295"}, "5971": {"model_id": "5971", "ARO_accession": "3007533", "model_param": {"blastp_bit_score": {"param_value": "1100", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "An MCR-4-type colistin resistance gene variant.", "model_sequences": {"sequence": {"8694": {"dna_sequence": {"partial": "0", "sequence": "GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGGTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGTTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCGGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGATATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG", "fmax": "1726", "accession": "NG_088453.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "WP_223106954.1", "sequence": "MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFGRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVFVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDRVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWISNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"}}}}, "model_name": "MCR-4.7", "ARO_category": {"36192": {"category_aro_name": "peptide antibiotic", "category_aro_cvterm_id": "36192", "category_aro_accession": "3000053", "category_aro_class_name": "Drug Class", "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."}, "41432": {"category_aro_name": "MCR phosphoethanolamine transferase", "category_aro_cvterm_id": "41432", "category_aro_accession": "3004268", "category_aro_class_name": "AMR Gene Family", "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."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "36968": {"category_aro_name": "colistin B", "category_aro_cvterm_id": "36968", "category_aro_accession": "3000624", "category_aro_class_name": "Antibiotic", "category_aro_description": "Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria."}, "36966": {"category_aro_name": "colistin A", "category_aro_cvterm_id": "36966", "category_aro_accession": "3000622", "category_aro_class_name": "Antibiotic", "category_aro_description": "Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria."}}, "ARO_name": "MCR-4.7", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "MCR-4.7", "ARO_id": "46304", "model_type_id": "40292"}, "5970": {"model_id": "5970", "ARO_accession": "3007531", "model_param": {"blastp_bit_score": {"param_value": "1500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13036": "T553K", "13037": "P601L", "13038": "M593T"}, "clinical": {"13036": "T553K", "13037": "P601L", "13038": "M593T"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "ARO_description": "PBP2x is a penicillin-binding protein and beta-lactam resistance enzyme. Mutations can cause resistance to some beta-lactam antibiotics.", "model_sequences": {"sequence": {"8693": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAATGGCAAAAATATGTTTTAGATTATGTTGTGCGCGATAGGAGAACTCCAGTCGAAAATCGCGTTCGAGTTGGACAAAATATGATGCTCTTAACTATCTTTATTTTCTTTATTTTCATTATTAATTTCATGATTATTATTGGAACAGATCAAAAGTTTGGAGTTAGTTTGTCAGAAGGGGCGAAGAAGGTTTATCAAGAAACCGTTACGATCCAAGCTAAGCGTGGGACCATTTATGATCGAAATGGTACAGCTATTGCAGTGGATTCTACGACTTATAGCATATACGCAATTTTGGATAAATCATTTGTCTCGGCTTCAGATGAAAAGTTATATGTACAACCTTCTCAGTATGAAACAGTAGCTGATATTTTAAAAAAGCATCTGGGAATGAAAAAAACAGATGTAATTAAACAGCTTAAGCGTAAAGGACTTTTCCAAGTCTCGTTTGGACCGTCAGGGTCTGGCATTTCATATAGTACTATGTCTACTATTCAAAAGGCTATGGAAGATGCCAAAATCAAGGGAATTGCTTTCACAACTAGTCCTGGTCGTATGTATCCAAATGGGACATTTGCTTCAGAATTTATAGGCCTAGCATCTCTAACAGAAGATAAAAAGACAGGTGTTAAGAGTTTAGTTGGAAAAACAGGTTTAGAAGCTTCTTTTGATAAAATTTTATCAGGTCAAGATGGTGTTATTACTTATCAAAAAGATCGAAATGGGACCACACTCTTGGGTACAGGTAAGACTGTCAAGAAAGCTATTGATGGCAAAGATATTTACACAACGCTATCTGAGCCTATCCAGACCTTCTTAGAAACCCAGATGGATGTTTTTCAAGCCAAATCAAATGGTCAGTTGGCCAGTGCAACACTTGTTAATGCTAAAACTGGTGAAATTTTGGCAACAACACAACGCCCCACTTATAATGCTGATACTCTGAAAGGACTTGAAAATACGAACTACAAATGGTACAGTGCACTTCATCAAGGAAATTTTGAACCAGGTTCAACCATGAAAGTGATGACTCTGGCAGCGGCTATTGATGATAAAGTTTTCAACCCAAACGAAACCTTTAGCAATGCTAATGGTTTGACAATTGCAGATGCTACTATTCAAGACTGGTCTATTAACGAAGGCATTTCCACAGGACAGTACATGAATTATGCACAAGGATTTGCCTTCTCAAGTAACGTTGGGATGACTAAACTTGAACAAAAAATGGGTAATGCAAAATGGATGAATTATTTGACGAAGTTCCGCTTTGGTTTTCCTACTCGTTTTGGTTTAAAAGATGAAGACGCAGGTATATTTCCTTCTGATAATATCGTGACTCAAGCTATGAGCGCTTTTGGTCAAGGGATTTCTGTAACCCAGATTCAAATGCTTAGAGCCTTTACTGCTATTTCTAATAATGGTGAGATGTTAGAGCCACAATTTATCAGTCAAATTTATGATCCTAACACAGCAAGTTTTAGAACGGCAAATAAAGAAATTGTTGGAAAACCTGTATCAAAAAAAGCCGCTAGTGAAACAAGACAATACATGATTGGTGTAGGAACAGACCCTGAGTTTGGAACACTCTATTCAAAAACATTTGGACCAATTATTAAAGTGGGTGATTTACCTGTTGCTGTTAAATCAGGAACAGCACAAATTGGTTCAGAAGATGGAAGTGGTTATCAAGATGGTGGATTGACTAACTATGTCTATTCGGTTGTGGCAATGGTGCCAGCTGATAAACCAGACTTTTTGATGTATGTTACTATGACTAAACCACAACATTTTGGTCCCCTTTTTTGGCAAGATGTGGTTAACCCAGTATTGGAAGAAGCATACTTAATGCAAGATACACTAACTAAGCCAGTAGTATCAGATGCTAATCGTCAAACAACTTATAAATTACCAAACTTTGTAGGAAAGAATCCTGGTGAGACATCAAGCGAGTTGCGTCGAAATCTTGTCCAGCCAGTTGTCCTTGGTACTGGCAGCAAGATCAAAAAAGTATCGCATCAGCCCGGTCAAACGTTAACAGAAAACCAACAAGTTCTCATATTATCAGACCGTTTTGTGGAGGTACCAGACATGTATGGCTGGACAAAATCCAATGTTAAAACCTTTGCTAAATGGACTGGGATAGACATCAGCTTTAAAGGAACAGATTCTGGTCGTGTTATGAAACAAAGTGTTGATGTTGGTAAGTCCTTGAAAAAAATAAAAAAAATGACCATTACTTTAGGAGATTAA", "fmax": "1375296", "accession": "CP072112.1", "fmin": "1373040", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptococcus pyogenes", "NCBI_taxonomy_id": "1314", "NCBI_taxonomy_cvterm_id": "36764"}, "protein_sequence": {"accession": "QTH61293.1", "sequence": "MKKWQKYVLDYVVRDRRTPVENRVRVGQNMMLLTIFIFFIFIINFMIIIGTDQKFGVSLSEGAKKVYQETVTIQAKRGTIYDRNGTAIAVDSTTYSIYAILDKSFVSASDEKLYVQPSQYETVADILKKHLGMKKTDVIKQLKRKGLFQVSFGPSGSGISYSTMSTIQKAMEDAKIKGIAFTTSPGRMYPNGTFASEFIGLASLTEDKKTGVKSLVGKTGLEASFDKILSGQDGVITYQKDRNGTTLLGTGKTVKKAIDGKDIYTTLSEPIQTFLETQMDVFQAKSNGQLASATLVNAKTGEILATTQRPTYNADTLKGLENTNYKWYSALHQGNFEPGSTMKVMTLAAAIDDKVFNPNETFSNANGLTIADATIQDWSINEGISTGQYMNYAQGFAFSSNVGMTKLEQKMGNAKWMNYLTKFRFGFPTRFGLKDEDAGIFPSDNIVTQAMSAFGQGISVTQIQMLRAFTAISNNGEMLEPQFISQIYDPNTASFRTANKEIVGKPVSKKAASETRQYMIGVGTDPEFGTLYSKTFGPIIKVGDLPVAVKSGTAQIGSEDGSGYQDGGLTNYVYSVVAMVPADKPDFLMYVTMTKPQHFGPLFWQDVVNPVLEEAYLMQDTLTKPVVSDANRQTTYKLPNFVGKNPGETSSELRRNLVQPVVLGTGSKIKKVSHQPGQTLTENQQVLILSDRFVEVPDMYGWTKSNVKTFAKWTGIDISFKGTDSGRVMKQSVDVGKSLKKIKKMTITLGD"}}}}, "model_name": "Streptococcus pyogenes PBP2x conferring resistance to beta-lactam antibiotics", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "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."}, "36981": {"category_aro_name": "ampicillin", "category_aro_cvterm_id": "36981", "category_aro_accession": "3000637", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "35981": {"category_aro_name": "amoxicillin", "category_aro_cvterm_id": "35981", "category_aro_accession": "0000064", "category_aro_class_name": "Antibiotic", "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."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "40661": {"category_aro_name": "Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics", "category_aro_cvterm_id": "40661", "category_aro_accession": "3003938", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics."}}, "ARO_name": "Streptococcus pyogenes PBP2x conferring resistance to beta-lactam antibiotics", "model_type": "protein variant model", "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.", "CARD_short_name": "Spyo_PBP2x_BLA", "ARO_id": "46302", "model_type_id": "40293"}, "5977": {"model_id": "5977", "ARO_accession": "3007561", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "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.", "model_sequences": {"sequence": {"8699": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGATACTTTTTGGCTTGATGGTGGTATTCGAATTTCGGCCATTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "798", "accession": "OK180617.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shewanella xiamenensis", "NCBI_taxonomy_id": "332186", "NCBI_taxonomy_cvterm_id": "39674"}, "protein_sequence": {"accession": "UBJ91323.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDTFWLDGGIRISAIEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "model_name": "OXA-1038", "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "37084": {"category_aro_name": "cefalotin", "category_aro_cvterm_id": "37084", "category_aro_accession": "3000704", "category_aro_class_name": "Antibiotic", "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."}, "35973": {"category_aro_name": "oxacillin", "category_aro_cvterm_id": "35973", "category_aro_accession": "0000056", "category_aro_class_name": "Antibiotic", "category_aro_description": "Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis."}, "35930": {"category_aro_name": "cloxacillin", "category_aro_cvterm_id": "35930", "category_aro_accession": "0000011", "category_aro_class_name": "Antibiotic", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}, "35990": {"category_aro_name": "meropenem", "category_aro_cvterm_id": "35990", "category_aro_accession": "0000073", "category_aro_class_name": "Antibiotic", "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."}}, "ARO_name": "OXA-1038", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "OXA-1038", "ARO_id": "46334", "model_type_id": "40292"}, "5976": {"model_id": "5976", "ARO_accession": "3007544", "model_param": {"blastp_bit_score": {"param_value": "1600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13087": "T86I", "13088": "T86K"}, "clinical": {"13087": "T86I", "13088": "T86K"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "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.", "model_sequences": {"sequence": {"8698": {"dna_sequence": {"partial": "0", "sequence": "ATGGAAGATAATACACAGAGTTATGACAAAATAAAACAACGTAATATTTCTGAAGAAATGAAAAAATCATTCGTCTCCTATGCCATGTCGGTTATTGTTTCACGTGCGTTGCCAGATGTGCGTGATGGTTTGAAACCAGTTCACCGCCGTATTTTATATGCGATGAATGATCTTGGTATGACAAGTGATAAACCTTATAAAAAATCTGCTCGTATTGTTGGTGAAGTAATTGGTAAGTATCACCCTCATGGTGATACAGCTGTTTATGATTCAATGGTACGTATGGCACAAGAATTTTCATATCGATATATGTTGATTGATGGTCACGGTAACTTCGGATCAATCGATGGAGATGGTGCGGCTGCGATGCGTTATACAGAAGCGCGTATGTCTAAAATCTCAATGGAATTAATTCGTGATATCAATAAGAATACTGTAGATTTTATTGATAACTATGATGGTGAAGAGCGTGAACCCGTTGTACTACCATCGCGTTTCCCTAATGTTCTTGTTAATGGTGGTACTGGGATTGCGGTTGGTATGGCAACAAATATTCCTCCTCATAATCTTGGAGAAGTAATTGATGCAACGATTGCATTAATCGATAACCCAGATATAACAATCAAAGAACTAATGGAAGATTATATTTTTGGTCCTGATTTTCCAACAGGGGCACTTTTACTTGGACGTAGTGGAATCAAGTCAGCGTTTGAAACAGGACGAGGTTCTGTAGTTATGCGGGCAAAAGTGGATATCGAAGAAATGAAGAATGGTAAACCACGAATTATTATTTCCGAAATCCCATATCAAGTTAATAAAGCTACTTTAGTAGAAAAAATCGCAACACTTGTTCGTGATAAAGAAATTGATGGAATCACAGACCTAAGAGATGAATCAAACCGTGAAGGAATTCGTATTGTAGTAGAACTACGAAGAGAAGTTCAAGCGGAAGTTGTATTAAACCAACTTTATCGTCTTACAGCACTCCAATCATCGTTTGGGGTGAATATGTTAGCACTTGTTAATGGAAGACCTGAGTTATTAAATCTATTACAAGTATTAAGTCACTATCGTGATCATCAAATTGAAATTGTTACACGTAGAACACAATTTGAATTGAAAAAAGCAGAAGATCGCGCACATATCCTACAAGGACTTATGATTGCACTTGATCATATTGATGAAGTTATTTCAATCATACGTTCATCCAAGGATGATCCAGAAGCGATTACTCGACTCAATGAAGCGTTTGATTTAACAGAAATTCAATCTAAAGCAGTATTAGATATGCAATTGCGTCGTTTGACCGGATTGCAACGTGATAAAGTTGAGAATGAATTCAATGAATTAACTATTCTAATTGTTGATTTAAAAGATATTTTAGCGAACCACGACCGATTGCTTACAATCATTAAAGATGAATTAATCGAAATCAAAACAAAATTTGGTGATGATCGTCGTTCTGAAATTGTAGAAGCTGATATTGATATGTTAGATGAAGACTTAATTCCAGTTGAAGATATTGTTGTTACGATGACAATGAATGGATATATCAAACGTACCACAGTTGATTCATTCAATACACAAAATCGCGGTGGAAAAGGTGTACGCGGTATTAGTACATACGATGAAGACACCGTTGATCAATTTATAGCGATGTCGACACATGATTATCTATTACTCTTTACAAACCTCGGAAAAGTTTACCGTATTCGCGGATTTAATGTACCGTCATCAAGCCGTACATCAAAAGGAATACCAGTTGTTAACTTATTAAACCTTACAGAAGGTGAAACCGTTAAAACGCTCGTTAAAGTTGCGAAAGATGACGAATCAAAATATGCATTCTTCGTTACAAAACAAGGTATTGTGAAACGTGTTGAAGTTCAAGAGTTTGAATCAATACGCCAAAACGGTAAAATTGCGATTACACTTCGTGAAGATGACGAACTCGTAGGTGTTCGCATGACAAACGGAGATAATGAAATCATTATCGGAGGAAGCAACGGTAAGGCCGTTCGATTCGATGAAAATGAAGTCCGTTCTATGGGACGTACAGCATCAGGTGTTATTGGATTTAATGTTGATGAAGGTGAAGTAGTAGGAATTGCTACTGACCGTGAAGGTCAATATATCCTAGCTGTAACCGAAAAAGGTTACGGTAAGCGTACTGACATCGCGGAATACCGACGCACCAAACGTGGGGCTAAGGGCGTTAAAACAGTAAACATTACTGAGAAGAATGGTAACCTTGTCTCACTTCGTGCAGTTAACGGTGATGAGGAAGCATTAATCATCTCTAATGAAGGAACTGTTATTCGTACAGAAATCAGTAACATCGGAATTTATGGACGATCAACGATTGGTGTTCGTTTGATTAACGTTGGTGAAACAGATTCTGTGTCGCAAGTTGCGATTCTTCAACCTACAGTTGAGGAACCAGATGAAGAACAAACAACAGATCAAGTAGAACCTGTTAATGAAAAAGAAATAGAAATTGCAGAGTAA", "fmax": "80047", "accession": "LR134439.1", "fmin": "77539", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Erysipelothrix rhusiopathiae", "NCBI_taxonomy_id": "1648", "NCBI_taxonomy_cvterm_id": "43311"}, "protein_sequence": {"accession": "VEH83056.1", "sequence": "MEDNTQSYDKIKQRNISEEMKKSFVSYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDTAVYDSMVRMAQEFSYRYMLIDGHGNFGSIDGDGAAAMRYTEARMSKISMELIRDINKNTVDFIDNYDGEEREPVVLPSRFPNVLVNGGTGIAVGMATNIPPHNLGEVIDATIALIDNPDITIKELMEDYIFGPDFPTGALLLGRSGIKSAFETGRGSVVMRAKVDIEEMKNGKPRIIISEIPYQVNKATLVEKIATLVRDKEIDGITDLRDESNREGIRIVVELRREVQAEVVLNQLYRLTALQSSFGVNMLALVNGRPELLNLLQVLSHYRDHQIEIVTRRTQFELKKAEDRAHILQGLMIALDHIDEVISIIRSSKDDPEAITRLNEAFDLTEIQSKAVLDMQLRRLTGLQRDKVENEFNELTILIVDLKDILANHDRLLTIIKDELIEIKTKFGDDRRSEIVEADIDMLDEDLIPVEDIVVTMTMNGYIKRTTVDSFNTQNRGGKGVRGISTYDEDTVDQFIAMSTHDYLLLFTNLGKVYRIRGFNVPSSSRTSKGIPVVNLLNLTEGETVKTLVKVAKDDESKYAFFVTKQGIVKRVEVQEFESIRQNGKIAITLREDDELVGVRMTNGDNEIIIGGSNGKAVRFDENEVRSMGRTASGVIGFNVDEGEVVGIATDREGQYILAVTEKGYGKRTDIAEYRRTKRGAKGVKTVNITEKNGNLVSLRAVNGDEEALIISNEGTVIRTEISNIGIYGRSTIGVRLINVGETDSVSQVAILQPTVEEPDEEQTTDQVEPVNEKEIEIAE"}}}}, "model_name": "Erysipelothrix rhusiopathiae gyrA with mutation conferring resistance to enrofloxacin", "ARO_category": {"35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "45604": {"category_aro_name": "enrofloxacin", "category_aro_cvterm_id": "45604", "category_aro_accession": "3007045", "category_aro_class_name": "Antibiotic", "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."}, "39876": {"category_aro_name": "fluoroquinolone resistant gyrA", "category_aro_cvterm_id": "39876", "category_aro_accession": "3003292", "category_aro_class_name": "AMR Gene Family", "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."}}, "ARO_name": "Erysipelothrix rhusiopathiae gyrA with mutation conferring resistance to enrofloxacin", "model_type": "protein variant model", "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.", "CARD_short_name": "Erhu_gyrA_ENR", "ARO_id": "46315", "model_type_id": "40293"}, "5975": {"model_id": "5975", "ARO_accession": "3007539", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off)."}}, "ARO_description": "APH(9)-Ic is a chromosomal-encoded aminoglycoside phosphotransferase in S. maltophilia.", "model_sequences": {"sequence": {"8697": {"dna_sequence": {"partial": "0", "sequence": "ATGTCATTCGCTTCGGCGCAGCATCTCGGCGAAGTCCTGCAACAATCCTATGGCATCACCCCCACCGCCGTGGTGCCACGCCCGGTGGGCGCCGACGCCAATGCCAGCGTGTATCGCGTCGATGCGCGGCACGGGCAGTGGTGGTTGAAATGCCGTACCTACCAGGTCGCCCCAGCGGTGTGGGACAGCCTGCATTGGATGCGCGGCACGCTGGGTATCGATGAGATCGTCGCGCCGTGGCCGGCGTTGACCGGTGGTGCGTCTGTGCAGCGCTGGGGATTGCAGTTCACCCTGTTCCCGTATGTGGAAGGCCAGTCCGGATTCGAGGCGGCGTTGAGCCGCACGCAGTGGAAACGGCTGGGGGAGGTGCTGCGGCGCCTGCATGGCGCGCAGTTGCCAGCGGAACTGCAGCAGGCACTGCCGATCGTACGGCTGGAAACCGCGGCGCTGGAGACCGTCGGGCAATGGTTGGCCGGCGAGGGCCTGGCGGCCGCGAAGGACGGGCTGGGCCGCGCATTCGTTTCGGTATGGGACCAGCAGCATGCGCGCATCGCGGCGCTGCATGCGCAGGCACGGGAGCTGCTAGCGGCGTTGCAGGACGCGCCGGTAGACCTGCATCTGTGCCACACCGATCTGCATGCCGGCAACCTGCTGATGGGCAATGACGGGGGCCTGCACCTGATCGATTGGGATGGTCTGTCGCTGGCCCCGCGCGAGCGTGACCTGATGTTCATCGGTGCCGCTGTTGGCGGGCGCTGGGGTCGCGAGAATCCACTGGGGTTCGAGGAGGGCTACGGCAGCGATCGCGGTGACCCGCGCTGGATCGCCTGGTACCGGCACTGGCGCATTCTGCAGGACCTGATCGAGTTCCAGCAGGTGCTGCTGGGCAGTGACGGGGAGGACCGATCGCCGCAGTTGCGCCGGCAGTCACTGCACTACCTGGGGGAGCAGTTCGCACCGGGCAATGTGTTCGATGCGGCGGAGCGGGTATATCGCGCGCTGGATCAGGTTCCAGGCCGTTGCCAGCATCGCCCCGGGTAG", "fmax": "1041", "accession": "ON693243.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Stenotrophomonas maltophilia", "NCBI_taxonomy_id": "40324", "NCBI_taxonomy_cvterm_id": "37076"}, "protein_sequence": {"accession": "WCI13726.1", "sequence": "MSFASAQHLGEVLQQSYGITPTAVVPRPVGADANASVYRVDARHGQWWLKCRTYQVAPAVWDSLHWMRGTLGIDEIVAPWPALTGGASVQRWGLQFTLFPYVEGQSGFEAALSRTQWKRLGEVLRRLHGAQLPAELQQALPIVRLETAALETVGQWLAGEGLAAAKDGLGRAFVSVWDQQHARIAALHAQARELLAALQDAPVDLHLCHTDLHAGNLLMGNDGGLHLIDWDGLSLAPRERDLMFIGAAVGGRWGRENPLGFEEGYGSDRGDPRWIAWYRHWRILQDLIEFQQVLLGSDGEDRSPQLRRQSLHYLGEQFAPGNVFDAAERVYRALDQVPGRCQHRPG"}}}}, "model_name": "APH(9)-Ic", "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35957": {"category_aro_name": "spectinomycin", "category_aro_cvterm_id": "35957", "category_aro_accession": "0000039", "category_aro_class_name": "Antibiotic", "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."}, "36292": {"category_aro_name": "APH(9)", "category_aro_cvterm_id": "36292", "category_aro_accession": "3000153", "category_aro_class_name": "AMR Gene Family", "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."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}}, "ARO_name": "APH(9)-Ic", "model_type": "protein homolog model", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "CARD_short_name": "APH(9)-Ic", "ARO_id": "46310", "model_type_id": "40292"}, "5974": {"model_id": "5974", "ARO_accession": "3007537", "model_param": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "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)."}, "snp": {"param_type": "single resistance variant", "param_value": {"13078": "A1401G", "13081": "C462T", "13080": "G1484T", "13083": "C1402T", "13082": "A514C"}, "clinical": {"13078": "A1401G", "13081": "C462T", "13080": "G1484T", "13083": "C1402T", "13082": "A514C"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q."}}, "ARO_description": "Point mutation in M. tuberculosis rrnS conferring resistance to kanamycin antibiotic.", "model_sequences": {"sequence": {"8696": {"dna_sequence": {"partial": "0", "sequence": "TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT", "fmax": "1473382", "accession": "NC_000962.3", "fmin": "1471845", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "model_name": "Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to kanamycin", "ARO_category": {"35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35932": {"category_aro_name": "amikacin", "category_aro_cvterm_id": "35932", "category_aro_accession": "0000013", "category_aro_class_name": "Antibiotic", "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."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth."}, "40277": {"category_aro_name": "16s rRNA with mutation conferring resistance to aminoglycoside antibiotics", "category_aro_cvterm_id": "40277", "category_aro_accession": "3003666", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides."}}, "ARO_name": "Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to kanamycin", "model_type": "rRNA gene variant model", "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.", "CARD_short_name": "Mtub_16rrnS_KAN", "ARO_id": "46308", "model_type_id": "40295"}}}