{"$update": {"3593": {"$update": {"model_sequences": {"$update": {"sequence": {"6129": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAAGCGCAAGTACATTTATTTTTTTTCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTATTGAGCAAATGAGGGAATTGGAAGCTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTCGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCGAAGGCAGCAATTCAGTACAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTCGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAGATTCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA", "fmax": "885", "accession": "KX620467.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645", "NCBI_taxonomy_cvterm_id": "36926"}, "protein_sequence": {"accession": "ANZ90381.1", "sequence": "MFFFKKSASTFIFFLCLPLNSFASQESNSIEQMRELEASFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKDSAKIAINAVYGSYK"}}}}}}}, "2859": {"$update": {"model_sequences": {"$update": {"sequence": {"6137": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA", "fmax": "1194", "accession": "KX354370.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "ANJ78206.1", "sequence": "MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"}}}}}}}, "627": {"$update": {"model_param": {"$insert": {"40494": {"param_value": {"9917": "S531fs"}, "param_type_id": "40494", "param_type": "frameshift mutation", "param_description": "A frameshift is a type of genetic mutation caused by a nucleotide insertion or deletion that does not equal 3 bases. This changes the grouping of codons and thus the reading frame during translation, resulting in an incomplete or inactive protein product. Many frameshift mutations generate downstream STOP codons, resulting in premature peptide translation termination. Frameshifts may also confer antibiotic resistance through partial or total protein loss-of-function. Frameshift mutations are included with relevant models when applicable, with the following notation: [wild-type AA][position]fs;[[wild-type AA][position]STOP], where AA is an amino acid. If the premature STOP codon position is unknown or does not exist, [wild-type AA][position]fs is sufficient. Termination can also be denoted as: Ter[position]fs. This parameter is currently not included in detection algorithms."}}}}}, "2865": {"$update": {"model_sequences": {"$update": {"sequence": {"6138": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA", "fmax": "90021", "accession": "LLSH01000109.1", "fmin": "88827", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "KSN86152.1", "sequence": "MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"}}}}}}}, "571": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}}}}}, "196": {"$update": {"model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "3649": {"$update": {"ARO_name": "Neisseria gonorrhoeae mtrR with mutation conferring resistance"}}, "1203": {"$update": {"model_param": {"$update": {"43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "3631": {"$update": {"ARO_name": "Neisseria gonorrhoeae pilQ gene conferring resistance to beta-lactam"}}, "1876": {"$update": {"model_sequences": {"$update": {"sequence": {"6134": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCGCTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "154350", "accession": "CXPA01000063.1", "fmin": "153489", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "CTQ11867.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}}}}, "386": {"$update": {"model_sequences": {"$update": {"sequence": {"6133": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGCCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCATCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "8215", "accession": "CEGG01000030.1", "fmin": "7354", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "CEP30258.1", "sequence": "MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLPGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTHLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}}}}, "36": {"$update": {"ARO_description": "Point mutation of Mycobacterium leprae gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.", "ARO_name": "Mycobacterium leprae gyrA conferring resistance to fluoroquinolones"}}, "3076": {"$update": {"model_sequences": {"$update": {"sequence": {"6117": {"dna_sequence": {"partial": "0", "sequence": "ATGAATGAAGGAAAAAATGAGGTCAGTACTTCAGCTGCTGGCCGGTTCGCATTCCCATCAAACGCCACGTTTGCCTTGGGGGATCGCGTACGCAAGAAGTCTGGCGCTGCTTGGCAGGGGCGCATTGTCGGGTGGTACTGCACAACACTTACCCCTGAAGGCTACGCCGTCGAGTCCGAATCTCACCCAGACTCAGTCCAGATTTATCCCATGACTGCGCTTGAACGGGTGGCCTGA", "fmax": "401", "accession": "EU339233.1", "fmin": "164", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "ABY55281.1", "sequence": "MNEGKNEVSTSAAGRFAFPSNATFALGDRVRKKSGAAWQGRIVGWYCTTLTPEGYAVESESHPDSVQIYPMTALERVA"}}}}}}}, "535": {"$update": {"ARO_name": "Morganella morganii gyrB conferring resistance to fluoroquinolones"}}, "3646": {"$update": {"ARO_name": "Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin"}}, "489": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}, "snp": {"$update": {"param_value": {"$insert": {"9962": "L79S"}}, "clinical": {"$insert": {"9962": "L79S"}}}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}}}}}, "212": {"$update": {"ARO_name": "Staphylococcus aureus parC conferring resistance to fluoroquinolones"}}, "2800": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}, "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."}, "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."}}}}}, "3651": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}, "43010": {"$update": {"param_type": "moderate confidence TB"}}}}}}, "24": {"$update": {"ARO_description": "FusB encodes a 2-domain zinc-binding protein that binds the ribosomal translocase EF-G, causing it to dissociate from the ribosome. This action increases the ribosomal turnover rate and confers resistance to fusidic acid. This protein is considered a FusB-type protein.", "ARO_category": {"$delete": ["36000", "39459"], "$insert": {"35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "43297": {"category_aro_name": "Target protecting FusB-type protein conferring resistance to Fusidic acid", "category_aro_cvterm_id": "43297", "category_aro_accession": "3005086", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid."}}}}}, "3348": {"$update": {"ARO_category": {"$insert": {"35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "category_aro_description": "Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30."}}}}}, "1710": {"$update": {"ARO_name": "Mycobacterium leprae gyrB conferring resistance to fluoroquinolones"}}, "696": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}}}}}, "851": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "43010": {"$update": {"param_type": "moderate confidence TB"}}, "snp": {"$update": {"param_value": {"$insert": {"9934": "K96M", "9930": "T100P", "9937": "H57Q", "9939": "G17S", "9928": "R157W", "9940": "V9A", "9935": "S164P", "9932": "C138W", "9931": "R140G", "9923": "L182S", "9924": "E174G", "9925": "L72P", "9926": "A161G", "9927": "V157G"}}, "clinical": {"$insert": {"9934": "K96M", "9930": "T100P", "9937": "H57Q", "9939": "G17S", "9928": "R157W", "9940": "V9A", "9935": "S164P", "9932": "C138W", "9931": "R140G", "9923": "L182S", "9924": "E174G", "9925": "L72P", "9926": "A161G", "9927": "V157G"}}}}, "40330": {"$update": {"param_value": {"$insert": {"9938": "D63Y,T142K"}}}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "40394": {"$update": {"param_value": {"$insert": {"9933": "Q122STOP"}}}}}}}}, "1812": {"$update": {"ARO_category": {"$update": {"41371": {"$update": {"category_aro_name": "KHM beta-lactamase", "category_aro_description": "KHM beta-lactamases are Class B beta-lactamases that can confer resistance to all classes of beta-lactams, except the monobactams."}}}}}}, "2131": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43010": {"$update": {"param_type": "moderate confidence TB"}}}}}}, "3364": {"$update": {"ARO_description": "A fusidic acid resistance determinant in Staphylococcus cohnii. This protein behaves akin to FusB as it is a FusB-type protein. It mediates dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.", "ARO_category": {"$delete": ["36000", "39459"], "$insert": {"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."}, "43297": {"category_aro_name": "Target protecting FusB-type protein conferring resistance to Fusidic acid", "category_aro_cvterm_id": "43297", "category_aro_accession": "3005086", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid."}}}}}, "1943": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "1947": {"$update": {"model_sequences": {"$update": {"sequence": {"6064": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGGTTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA", "fmax": "876", "accession": "KP050493.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Proteus mirabilis", "NCBI_taxonomy_id": "584", "NCBI_taxonomy_cvterm_id": "36771"}, "protein_sequence": {"accession": "AJO16046.1", "sequence": "MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLVNYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"}}}}}}}, "1197": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "1696": {"$update": {"ARO_name": "Salmonella serovars gyrB conferring resistance to fluoroquinolones"}}, "1592": {"$update": {"model_sequences": {"$update": {"sequence": {"6119": {"dna_sequence": {"partial": "0", "sequence": "TTGAAAGTATCATTGATGGCTGCGAAAGCGAAAAACGGCGTGATTGGTTGCGGTCCAGACATACCCTGGTCCGCGAAAGGGGAGCAGCTACTTTTTAAAGCATTGACCTACAATCAGTGGCTTCTGGTGGGTCGCAAGACGTTTGAATCTATGGGCGCACTCCCCAATAGGAAATACGCGGTCGTTACCCGCTCAGGTTGGACATCAAATGATGACAATGTAGTTGTATTTCAGTCAATCGAAGAGGCCATGGACAGGCTAGCTGAATTCACCGGTCACGTTATAGTGTCTGGTGGCGGAGAAATTTACCGAGAAACATTACCCATGGCCTCTACGCTCCACTTATCGACGATCGACATCGAGCCAGAGGGGGATGTTTTCTTCCCGAGTATTCCAAATACCTTCGAAGTTGTTTTTGAGCAACACTTTACTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGTTAA", "fmax": "1091", "accession": "KF921535.1", "fmin": "617", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AHK10285.1", "sequence": "MKVSLMAAKAKNGVIGCGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSGWTSNDDNVVVFQSIEEAMDRLAEFTGHVIVSGGGEIYRETLPMASTLHLSTIDIEPEGDVFFPSIPNTFEVVFEQHFTSNINYCYQIWKKG"}}}}}}}, "2405": {"$update": {"ARO_name": "Neisseria gonorrhoeae parC conferring resistance to fluoroquinolones"}}, "2248": {"$update": {"ARO_description": "A specific fusidic acid resistance gene conferring intrinsic resistance in the bacteria Staphylococcus saprophyticus. FusD behaves by causing dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid. It is considered a FusB-type protein.", "ARO_category": {"$delete": ["36000", "39459"], "$insert": {"35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "43297": {"category_aro_name": "Target protecting FusB-type protein conferring resistance to Fusidic acid", "category_aro_cvterm_id": "43297", "category_aro_accession": "3005086", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid."}}}}}, "2386": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}}}}}, "1562": {"$update": {"ARO_description": "ANT(6)-Ia/aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis"}}, "2070": {"$update": {"model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "912": {"$update": {"model_sequences": {"$update": {"sequence": {"6135": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "2842857", "accession": "CP001891.1", "fmin": "2841996", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola At-22", "NCBI_taxonomy_id": "640131", "NCBI_taxonomy_cvterm_id": "43310"}, "protein_sequence": {"accession": "ADC58623.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}}}}, "3629": {"$update": {"ARO_name": "Neisseria gonorrhoeae PBP1 conferring resistance to beta-lactam"}}, "1176": {"$update": {"model_param": {"$update": {"43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}}}}}, "1237": {"$update": {"model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "1339": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "143": {"$update": {"model_sequences": {"$update": {"sequence": {"6071": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAAGGTTGGATGAAATGCGGATTGGCCGGAGCCGTGGTGCTGATGGCGAGTTTTTGGGGCGGCAGCGTGCGGGCGGCGGGGATCTCCCTCAAGCAGGTGAGCGGCCCTGTCTATGTGGTGGAGGATAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACTGCGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGTTGCACAAGCTGATCAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTTGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGATCTGCCGCTGGTGCTGCCGAACGTGGTGCACGATGGCGACTTCAAGCTGCAAGATGGCAAGGTGCGTGCCTTCTATGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGAGTATCCGCAGACCATCGAGCGGCTCAAGGCGATGAAGTTGCCGATCAAGACGGTGATCGGCGGTCACGACTCACCGCTGCACGGCCCCGAGCTGATTGATCACTACGAAGCGCTGATCAAGGCCGCTGCTCATTCATAA", "fmax": "765", "accession": "AY227053.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Aeromonas jandaei", "NCBI_taxonomy_id": "650", "NCBI_taxonomy_cvterm_id": "42604"}, "protein_sequence": {"accession": "AAP69915.1", "sequence": "MMKGWMKCGLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSMVYFGAKGVTAVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFKLQDGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKEYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAAHS"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "500"}}}}}}, "1267": {"$update": {"model_sequences": {"$update": {"sequence": {"6131": {"dna_sequence": {"partial": "0", "sequence": "ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACTGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAGAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTACGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG", "fmax": "660", "accession": "NG_050503.1", "fmin": "15", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter braakii", "NCBI_taxonomy_id": "57706", "NCBI_taxonomy_cvterm_id": "39584"}, "protein_sequence": {"accession": "WP_063866081.1", "sequence": "MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLRDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGTTFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"}}}}}}}, "2853": {"$update": {"model_sequences": {"$update": {"sequence": {"6136": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA", "fmax": "1294", "accession": "NG_051744.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "WP_040184286.1", "sequence": "MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"}}}}}}}, "3745": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "2148": {"$update": {"ARO_name": "Ureaplasma urealyticum  gyrB conferring resistance to fluoroquinolones"}}, "1354": {"$update": {"model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "1574": {"$update": {"model_param": {"$update": {"43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "43010": {"$update": {"param_type": "moderate confidence TB"}}}}}}, "3403": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "_timestamp": "2020-08-06T12:48:31+00:00", "2132": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}}}}}, "1935": {"$update": {"model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "127": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}}}}}, "2278": {"$update": {"ARO_name": "Bifidobacterium bifidum ileS conferring resistance to mupirocin"}}, "3268": {"$update": {"ARO_name": "Clostridioides difficile gyrB conferring resistance to fluoroquinolones"}}, "100": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}}}}}, "660": {"$update": {"ARO_name": "Streptococcus pneumoniae parC conferring resistance to fluoroquinolones"}}, "1849": {"$update": {"model_param": {"$update": {"42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "329": {"$update": {"model_sequences": {"$update": {"sequence": {"6063": {"dna_sequence": {"partial": "0", "sequence": "ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAAAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA", "fmax": "1011", "accession": "AB976602.1", "fmin": "135", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "BAP18874.1", "sequence": "MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAKLSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"}}}}}}}, "1432": {"$update": {"model_param": {"$update": {"43012": {"$update": {"param_type": "no association with resistance TB"}}, "43010": {"$update": {"param_type": "moderate confidence TB"}}}}}}, "2270": {"$update": {"ARO_name": "Staphylococcus aureus mupA conferring resistance to mupirocin"}}, "2215": {"$update": {"ARO_name": "Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolones"}}, "1642": {"$update": {"ARO_category": {"$insert": {"36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}}}}}, "2083": {"$update": {"ARO_name": "Mycoplasma hominis parC conferring resistance to fluoroquinolones"}}, "2315": {"$update": {"ARO_name": "Acinetobacter baumannii parC conferring resistance to fluoroquinolones"}}, "2235": {"$update": {"ARO_category": {"$update": {"41388": {"$update": {"category_aro_name": "SPG beta-lactamase"}}}}}}, "_version": "3.1.0", "1731": {"$update": {"model_sequences": {"$update": {"sequence": {"6082": {"dna_sequence": {"partial": "0", "sequence": "ATGAGTAAAGATATTAAACAAGTAATCGAGATAGCAAAAAAACACAATCTTTTTCTAAAAGAAGAAACGATACAGTTTAATGAATCAGGGCTTGATTTTCAAGCTGTTTTTGCACAAGATAATAATGGAATTGATTGGGTTCTAAGATTGCCTAGACGGGAAGATGTGATGCCTAGAACAAAGGTAGAAAAACAAGCTTTGGATTTGGTAAATAAGTACGCTATATCCTTTCAGGCACCAAACTGGATCATTTACACAGAGGAACTAATAGCTTATAAAAAGTTAGATGGTGTGCCAGCAGGTACGATAGATCATAACATAGGTAACTATATTTGGGAGATAGACATAAATAATGTTCCAGAATTATTTCACAAGTCGCTAGGCAGGGTGTTAGCAGAGCTTCATAGCATACCTAGTAATAAAGCCGCAGCGCTTGATCTTGTAGTACACACACCAGAAGAAGCAAGAATGTCAATGAAGCAGCGTATGGATGCAGTAAGAGCAAAGTTCGGAGTAGGTGAGAATCTATGGAACAGATGGCAAGCGTGGTTGAATGATGATGATATGTGGCCTAAGAAAACTGGACTGATTCATGGAGATGTACATGCCGGACATACTATGATTGATAAGGATGCCAATGTGACTGGATTAATCGATTGGACTGAAGCGAAGGTTACAGATGTTTCGCATGACTTTATTTTCAACTATAGAGCTTTTGGGGAAGAAGGGTTAGAAGCTTTAATTCTCGCTTATAAGGAAATTGGTGGATATTACTGGCCTAAAATGAAAGAGCATATTATCGAACTTAATGCAGCATACCCAGTTTCAATCGCTGAGTTTGCATTAGTGTCTGGAATTGAGGAATATGAGCAGATGGCAAAGGAAGCATTGGAAGTACAAGGTTCGTAA", "fmax": "2067", "accession": "D85892.1", "fmin": "1158", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "BAA12910.1", "sequence": "MSKDIKQVIEIAKKHNLFLKEETIQFNESGLDFQAVFAQDNNGIDWVLRLPRREDVMPRTKVEKQALDLVNKYAISFQAPNWIIYTEELIAYKKLDGVPAGTIDHNIGNYIWEIDINNVPELFHKSLGRVLAELHSIPSNKAAALDLVVHTPEEARMSMKQRMDAVRAKFGVGENLWNRWQAWLNDDDMWPKKTGLIHGDVHAGHTMIDKDANVTGLIDWTEAKVTDVSHDFIFNYRAFGEEGLEALILAYKEIGGYYWPKMKEHIIELNAAYPVSIAEFALVSGIEEYEQMAKEALEVQGS"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "600"}}}}}}, "2109": {"$update": {"ARO_name": "Mycobacterium tuberculosis gyrB mutant conferring resistance to fluoroquinolones", "model_param": {"$update": {"43010": {"$update": {"param_type": "moderate confidence TB"}}, "43013": {"$update": {"param_type": "indeterminate confidence TB"}}, "43012": {"$update": {"param_type": "no association with resistance TB"}}, "43011": {"$update": {"param_type": "minimal confidence TB"}}, "42998": {"$update": {"param_type": "high confidence TB"}}}}}}, "1450": {"$update": {"ARO_name": "Escherichia coli parC conferring resistance to fluoroquinolones"}}, "2271": {"$update": {"ARO_name": "Staphylococcus aureus mupB conferring resistance to mupirocin"}}, "1965": {"$update": {"model_sequences": {"$update": {"sequence": {"6132": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "121152", "accession": "FLES01000010.1", "fmin": "120291", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "SAU22663.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}}}}, "1386": {"$update": {"model_sequences": {"$update": {"sequence": {"6083": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCAATTTGATTAACGGAAAAATACCAAATCAAGCGATTCAAACATTAAAAATCGTAAAAGATTTATTTGGAAGTTCAATAGTTGGAGTATATCTATTTGGTTCAGCAGTAAATGGTGGTTTACGCATTAACAGCGATGTAGATGTTCTAGTCGTCGTGAATCATAGTTTACCTCAATTAACTCGAAAAAAACTAACAGAAAGACTAATGACTATATCAGGAAAGATTGGAAATACGGATTCTGTTAGACCACTTGAAGTTACGGTTATAAATAGGAGTGAAGTTGTCCCTTGGCAATATCCTCCAAAAAGAGAATTTATATACGGTGAGTGGCTCAGGGGTGAATTTGAGAATGGACAAATTCAGGAACCAAGCTATGATCCTGATTTGGCTATTGTTTTAGCACAAGCAAGAAAGAATAGTATTTCTCTATTTGGTCCTGATTCTTCAAGTATACTTGTCTCCGTACCTTTGACAGATATTCGAAGAGCAATTAAGGATTCTTTGCCAGAACTAATTGAGGGGATAAAAGGTGATGAGCGTAATGTAATTTTAACCCTAGCTCGAATGTGGCAAACAGTGACTACTGGTGAAATTACCTCGAAAGATGTCGCTGCAGAATGGGCTATACCTCTTTTACCTAAAGAGCATGTAACTTTACTGGATATAGCTAGAAAAGGCTATCGGGGAGAGTGTGATGATAAGTGGGAAGGACTATATTCAAAGGTGAAAGCACTCGTTAAGTATATGAAAAATTCTATAGAAACTTCTCTCAATTAG", "fmax": "1113", "accession": "X02588.1", "fmin": "330", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus aureus", "NCBI_taxonomy_id": "1280", "NCBI_taxonomy_cvterm_id": "35508"}, "protein_sequence": {"accession": "CAA26428.1", "sequence": "MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN"}}}}}}}, "2250": {"$update": {"ARO_description": "FusC is a fusidic acid resistance gene enabling ribosomal translocase EF-G dissociation from the ribosome that has been detected in Staphylococcus aureus and Staphylococcus intermedius. Its mechanism is believed to be similar to fusB due to its high level of sequence homology. It is considered a FusB-type protein.", "ARO_category": {"$delete": ["36000", "39459"], "$insert": {"35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "43297": {"category_aro_name": "Target protecting FusB-type protein conferring resistance to Fusidic acid", "category_aro_cvterm_id": "43297", "category_aro_accession": "3005086", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid."}}}}}, "2104": {"$update": {"ARO_name": "Ureaplasma urealyticum parC conferring resistance to fluoroquinolones"}}}, "$delete": ["2292"], "$insert": {"3773": {"model_id": "3773", "ARO_accession": "3003169", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases.", "model_sequences": {"sequence": {"6065": {"dna_sequence": {"partial": "0", "sequence": "ATGGTGACAAAGAGAGTGCAACGGATGATGTTYGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGAAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA", "fmax": "876", "accession": "KP128034.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AJU57235.1", "sequence": "MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPEGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-161", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39746", "model_name": "CTX-M-161", "model_type_id": "40292"}, "3772": {"model_id": "3772", "ARO_accession": "3005033", "model_param": {"blastp_bit_score": {"param_value": "615", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FLC-1 is part of the FRI beta-lactamase family. It is a class A carbapenem-hydrolyzing beta-lactamase from Enterobacter cloacae.", "model_sequences": {"sequence": {"6062": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAAAAAAATGCGAAAAAATGCGATTATTCTTTCTTTTTCGCTCTGCCTTCCTTTTGCTTCATCTAACTCATTTGCAAATCAGGAAAGGAATGGCCTGGCTCAAATTAAGGAACTGGAAACTGTTTTTGGAGGGCGGATAGGTGTTTATCTTTTAAATACAGAAAATGGGAAAGAGTTTTCCTACAGGCAAAATGAGAGATTTCCTTTATGCAGTTCATTTAAGGTGTTCTTAGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTTTTTCTCTTAATGATACGGTAGAGTATTCCGATCGTGTTATGGAGAAGCATTCTCCTGTATCAGAAAAATACCTAGAAACGGGTGCAAGCGTTCAGACTTTGGCTATGGCAGCAATTCAGTACAGTGATAATGGAGCGTCTAATCTATTAATGGAAAGATACGTCGGAGGTCCTGAAGGTTTGACTGCATTTATGCGATCAACGGGAGACACGGAGTTCAGGCTTGATCGCTGGGAGTTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGATACTTCAACTCCGAAAGCAGTAGCAATGAGCCTAAAAAATATTGCATTTGGTTCTGTACTTGATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTCAAGGAAACACGACTGGCAATGCGCGAGTCAGAGCCGCAGTTCCTGATAAATGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCTGATTCCAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTACTAATCAAAACGATAAACATGATGAAACAATAATTAAAAATGCTGCAAAAATTGCTATAAATGCAGTGTATGGAAGTTATAAATGA", "fmax": "897", "accession": "MG309750.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "ATX60370.1", "sequence": "MLKKMRKNAIILSFSLCLPFASSNSFANQERNGLAQIKELETVFGGRIGVYLLNTENGKEFSYRQNERFPLCSSFKVFLAASVLKKTQDKSFSLNDTVEYSDRVMEKHSPVSEKYLETGASVQTLAMAAIQYSDNGASNLLMERYVGGPEGLTAFMRSTGDTEFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSVLDAKNKALLQDWLQGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDSNSPAVIAVYTTRTNQNDKHDETIIKNAAKIAINAVYGSYK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FLC-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43226", "model_name": "FLC-1", "model_type_id": "40292"}, "3771": {"model_id": "3771", "ARO_accession": "3005032", "model_param": {"blastp_bit_score": {"param_value": "605", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-9 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.", "model_sequences": {"sequence": {"6061": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTAAAAAAAAGTGCAAGTACATTTGTTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCCCAGGAAAGTAATGGTGTTGAGCAAATGAAGGAATTGGAAAATTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAACAGTGGCTATGAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTACTAAATAA", "fmax": "118807", "accession": "AP019633.1", "fmin": "117922", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645", "NCBI_taxonomy_cvterm_id": "36926"}, "protein_sequence": {"accession": "BBJ65425.1", "sequence": "MFFLKKSASTFVFLLCLPLNSFASQESNGVEQMKELENSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKTVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-9", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43225", "model_name": "FRI-9", "model_type_id": "40292"}, "3770": {"model_id": "3770", "ARO_accession": "3005031", "model_param": {"blastp_bit_score": {"param_value": "615", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-8 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter sp. 18A13. It is from a plasmid.", "model_sequences": {"sequence": {"6060": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAAAAAAATGCGAAAAAATGCGATTATTCTTTCTTTTTCGCTCTGCCTTCCTTTTGCTTCATCTAACTCATTTGCAAATCAGGAAAGGAATGGCCTGGCTCAAATTAAGGAACTGGAAACTGTTTTTGGAGGGCGGATAGGTGTTTATCTTTTAAATACAGAAAATGGGAAAGAGTTTTCCTACAGGCAAAATGAGAGATTTCCTTTATGCAGTTCATTTAAGGTGTTCTTAGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTTTTTCTCTTAATGATACGGTAGAGTATTCCGGTCGTGTTATGGAGAAGCATTCTCCTGTATCAGAAAAATACCTAGAAACGGGTGCAAGCGTTCAGACTTTGGCTATGGCAGCAATTCAGTACAGTGATAATGGAGCGTCTAATCTATTAATGGAAAGATACGTCGGAGGTCCTGAAGGTTTGACTGCATTTATGCGATCAACGGGAGACACGGAGTTCAGGCTTGATCGCTGGGAGTTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGATACTTCAACTCCGAAAGCAGTAGCAATGAGCCTAAAAAATATTGCATTTGGTTCTGTACTTGATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTCAAGGAAACACGACTGGCAATGCGCGAGTCAGAGCCGCAGTTCCTGATAAATGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCTGATTCCAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTACTAATCAAAACGATAAACATGATGAAACAATAATTAAAAATGCTGCAAAAATTGCTATAAATGCAGTGTATGGAAGTTATAAATGA", "fmax": "147759", "accession": "AP019635.1", "fmin": "146862", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter sp. 18A13", "NCBI_taxonomy_id": "2565914", "NCBI_taxonomy_cvterm_id": "43224"}, "protein_sequence": {"accession": "BBJ69931.1", "sequence": "MLKKMRKNAIILSFSLCLPFASSNSFANQERNGLAQIKELETVFGGRIGVYLLNTENGKEFSYRQNERFPLCSSFKVFLAASVLKKTQDKSFSLNDTVEYSGRVMEKHSPVSEKYLETGASVQTLAMAAIQYSDNGASNLLMERYVGGPEGLTAFMRSTGDTEFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSVLDAKNKALLQDWLQGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDSNSPAVIAVYTTRTNQNDKHDETIIKNAAKIAINAVYGSYK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-8", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43223", "model_name": "FRI-8", "model_type_id": "40292"}, "3777": {"model_id": "3777", "ARO_accession": "3003649", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamase, no other information available", "model_sequences": {"sequence": {"6069": {"dna_sequence": {"partial": "0", "sequence": "ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCTTCCAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA", "fmax": "876", "accession": "KP727572.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AKR53960.1", "sequence": "MMTQSIRRSMLTVMATLPLLFSSATLHAQASSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-165", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40259", "model_name": "CTX-M-165", "model_type_id": "40292"}, "3776": {"model_id": "3776", "ARO_accession": "3003648", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamase, no other information available", "model_sequences": {"sequence": {"6068": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAAATCACTGCGCAAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA", "fmax": "876", "accession": "KP727571.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Proteus mirabilis", "NCBI_taxonomy_id": "584", "NCBI_taxonomy_cvterm_id": "36771"}, "protein_sequence": {"accession": "AKR53959.1", "sequence": "MVKKSLRKFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-164", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40258", "model_name": "CTX-M-164", "model_type_id": "40292"}, "3775": {"model_id": "3775", "ARO_accession": "3003647", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamase, no other information available", "model_sequences": {"sequence": {"6067": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAAATCACTGAGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA", "fmax": "876", "accession": "KP681698.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AKO63214.1", "sequence": "MVKKSLSQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-163", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40257", "model_name": "CTX-M-163", "model_type_id": "40292"}, "3774": {"model_id": "3774", "ARO_accession": "3003646", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamase, no other information available", "model_sequences": {"sequence": {"6066": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAAATCACTGAGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA", "fmax": "876", "accession": "KP681697.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella oxytoca", "NCBI_taxonomy_id": "571", "NCBI_taxonomy_cvterm_id": "36788"}, "protein_sequence": {"accession": "AKO63213.1", "sequence": "MVKKSLSQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-162", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40256", "model_name": "CTX-M-162", "model_type_id": "40292"}, "3751": {"model_id": "3751", "ARO_accession": "3001044", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "TEM-181 is a beta-lactamase.", "model_sequences": {"sequence": {"6042": {"dna_sequence": {"partial": "1", "sequence": "CAAACTCTTTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGA", "fmax": "1061", "accession": "NG_050218.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacteria", "NCBI_taxonomy_id": "2", "NCBI_taxonomy_cvterm_id": "35506"}, "protein_sequence": {"accession": "WP_000027060.1", "sequence": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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-181", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37424", "model_name": "TEM-181", "model_type_id": "40292"}, "3804": {"model_id": "3804", "ARO_accession": "3005064", "model_param": {"blastp_bit_score": {"param_value": "800", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cprS is part of a two-component regulatory system that, with its counterpart cprR, induces the Arn operon in the presence of cationic peptides to confer resistance.", "model_sequences": {"sequence": {"6099": {"dna_sequence": {"partial": "0", "sequence": "ATGAAACGCGGCCTGAGCCTGATCCCCATCGTCGGCGGCGGCGTCACCCTGATCCTCGCCGGGGTGTTGCTGGTCTACACGCGCATGCTCGGCGACTACGGCGAGACCGGCGCCCTCTACCTGCTCAGCATGATGATGGAAGAGGAAGGGCTGTACTTCGCCCAGCGCTACCAGGAAGACCCGGCTACGCCGGCGCCGGACAGCTACTACTTCAAGGGCAGCGTCGGCACCGCGGGGCTGCCGCCGAAACTCAGGGAGATGCTCGACACCCCGCCCTACAAGAGCATCGGCGCCATGCAACTGCTCGGCAACTGGGACGACGATGACGAAGAGGAGGATGACGACGCGCCCAGCGACGATGCCTACGTGGTGGTCCGCCAGCCACTGGCCGACGGCAAGACGCTCTACCTCTACGACAACGACGCCGCCGGCAGCATCGACACGCCGCTGTCCGACGCCATCATCGACGCCCGCGTCAGGCAGACCTGGATCGTCACCCTGTCGGTCACCCTGCCTTCGCTGGCCGCCGTCGGCCTGCTGGTCTGGTTCATCGTCGCGCCGTTGCGCAAGCTGACGCGCTGGTCGATGACCCTCGACGACCTCGCCCCGGACAGCCAGCGGCCGCGCTTCAACTACCGCGAACTCAACGTGCTGGCGGATACCCTGTGGAACAGCGTGACCCGGATCAAGGACTTCAGCCAGCGCGAGGAGCGCTTCCTGCGCTACGCCAGCCATGAGCTGCGCACCCCGCTGGCGGTGATCGGCATGAACCTGGAGTTGCTCGACCAACCCGGCCGCGCGCCCTCCCCGCATGCCTTGCAACGCATCCGCCGCTCGGCGCTGGGCATGCAGCAGATGACCGAGACCCTGCTCTGGCTCAGCCGCGAGAGCGGCGAACTGCGCGACGACGGACACATCGAGGTCGGCCGCCTGCTGGAGGAACTGCTCGAGGAACAGCAGGCGCTGAGCCAGCGCCGCGGCCTGACCTTCCACCTCGACGTGGAGCCACACAGCCTGCCGCAGACCCGCGCACGGATCATCATCGGCAACCTGCTGCGCAACGCCCTGCAGTACAGCGACGAGGGCGTGGTGGAAATCGTCGTGCGCGACCGCAGCCTGCTGATCAGCAACCCCATCGGTGCGGCCCAGGGCACGGAGGAGTCGATGGCGTTCGGTTATGGCCTGGGCCTCGACCTGGTCCAGCGCCTGTGCCAGAAGAGTGGCTGGCGCCTGCATTACAGCAGCGACGAGCAGCGCTTCCGCTGCGAGCTGCTGTTCCCCGCCACGCCGGACTGA", "fmax": "3452801", "accession": "AE004091.2", "fmin": "3451505", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "AAG06466.1", "sequence": "MKRGLSLIPIVGGGVTLILAGVLLVYTRMLGDYGETGALYLLSMMMEEEGLYFAQRYQEDPATPAPDSYYFKGSVGTAGLPPKLREMLDTPPYKSIGAMQLLGNWDDDDEEEDDDAPSDDAYVVVRQPLADGKTLYLYDNDAAGSIDTPLSDAIIDARVRQTWIVTLSVTLPSLAAVGLLVWFIVAPLRKLTRWSMTLDDLAPDSQRPRFNYRELNVLADTLWNSVTRIKDFSQREERFLRYASHELRTPLAVIGMNLELLDQPGRAPSPHALQRIRRSALGMQQMTETLLWLSRESGELRDDGHIEVGRLLEELLEEQQALSQRRGLTFHLDVEPHSLPQTRARIIIGNLLRNALQYSDEGVVEIVVRDRSLLISNPIGAAQGTEESMAFGYGLGLDLVQRLCQKSGWRLHYSSDEQRFRCELLFPATPD"}}}}, "ARO_category": {"41433": {"category_aro_name": "pmr phosphoethanolamine transferase", "category_aro_cvterm_id": "41433", "category_aro_accession": "3004269", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane."}, "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."}, "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."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "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": "cprS", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43268", "model_name": "cprS", "model_type_id": "40292"}, "3779": {"model_id": "3779", "ARO_accession": "3005035", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Yrc-1 is a ampC-like beta-lactamase that confers resistance to penams and cephalosporins. It is an ambler class C beta-lactamase.", "model_sequences": {"sequence": {"6072": {"dna_sequence": {"partial": "0", "sequence": "ATGATGCATAAAACCCTTTCCTGTGCGCTGCTGCTCGTCGCGTCAGGTTCCACGTTTGCCACGCCTCAAACGGAAAAAAAACTCAGTGGAATTGTTGATAACGTTGTTATTCCTTTGATGAAAGAACAGGCCATTCCCGGCATGGCGGTGGCGGTGATCTATCAGGGCCAACCTTACTACTTTACCTGGGGAATGGCTGATGTCGCAGGCAAACAGCCTGTTACGCAGCAGACGTTATTCGAGCTCGGCTCCGTGAGTAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCTCGTGGGGAAATTAAACTTAGTGATCCAGTGAGTAAATACTGGCCAGCGCTTTCCGGGAAACAATGGGAAGGGATTAGTTTGCTGAATTTGGCAACCTATACCGCTGGTGGCTTGCCGCTCCAGGTACCGGATAACATTACTGATGAGACGTCATTGCAGAATTACTATGAAACCTGGCAGCCACAGTGGGCTCCGGGCACCAAGCGTTTTTATTCAAACGCCAGTATTGGGATGTTTGGCAAACTGGCGGTTAAACCTTCAGGCATGAGCTTTGAGCAGGCGATGAACAAACGCGTGTTCCAGCCATTGAATCTCACGCATACTTGGATACATGTTCCTGAACGTGAAGAAAAACACTATGCGTGGGGCTATCGCGATGGGAAAGCCGTTCATGTTTCTCCGGGGATGCTGGACGCTGAAGCCTACGGCGTGAAATCCTCAATAAAGGATATGGCAAGCTGGGTGCGGGCTAACATGACGCCTTCTGAAGTAAAAGATGCCTCGCTGCAAAAGGGGATTTTGCTTGCCCAGTCGCGGTACTTGCAAGTGGGTGACATGTATCAGGGGTTGGGCTGGGAAATGCTGAACTGGCCGATGAAAGCAACAATCGCGGTCGGCGGTAGCGATAATAAAGTCGCACTCGCGCCGCTAAGTGCGGTAGAAATTAACCCGCCAGCGCCAGCATTAAATAGCTCGTGGGTACATAAAACTGGCTCAACCGGCGGATTTGGAAGCTACGTGGCTTTCATTCCCGAGAAGAATCTCGGCATCGTGATGCTGGCGAACAAAAGTTATCCTAACCCTGCGCGTGTCGAAGCAGCTTACCGCATCCTTGAAGCTTTGTCCGTGGAATAG", "fmax": "1532", "accession": "DQ185144.1", "fmin": "380", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Yersinia ruckeri", "NCBI_taxonomy_id": "29486", "NCBI_taxonomy_cvterm_id": "42660"}, "protein_sequence": {"accession": "ABA70720.1", "sequence": "MMHKTLSCALLLVASGSTFATPQTEKKLSGIVDNVVIPLMKEQAIPGMAVAVIYQGQPYYFTWGMADVAGKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPVSKYWPALSGKQWEGISLLNLATYTAGGLPLQVPDNITDETSLQNYYETWQPQWAPGTKRFYSNASIGMFGKLAVKPSGMSFEQAMNKRVFQPLNLTHTWIHVPEREEKHYAWGYRDGKAVHVSPGMLDAEAYGVKSSIKDMASWVRANMTPSEVKDASLQKGILLAQSRYLQVGDMYQGLGWEMLNWPMKATIAVGGSDNKVALAPLSAVEINPPAPALNSSWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPARVEAAYRILEALSVE"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "43232": {"category_aro_name": "YRC Beta-lactamase", "category_aro_cvterm_id": "43232", "category_aro_accession": "3005034", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "YRC is a ambler class C beta-lactamase from Yersinia ruckeri. It confers resistance penams and cephalosporins."}}, "ARO_name": "Yrc-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43233", "model_name": "Yrc-1", "model_type_id": "40292"}, "3778": {"model_id": "3778", "ARO_accession": "3003650", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamase, no other information available", "model_sequences": {"sequence": {"6070": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGTTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA", "fmax": "876", "accession": "LN830266.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "CFW94147.1", "sequence": "MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLVELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"}}}}, "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."}, "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."}, "36025": {"category_aro_name": "CTX-M beta-lactamase", "category_aro_cvterm_id": "36025", "category_aro_accession": "3000016", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam."}}, "ARO_name": "CTX-M-166", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40260", "model_name": "CTX-M-166", "model_type_id": "40292"}, "3755": {"model_id": "3755", "ARO_accession": "3005010", "model_param": {"blastp_bit_score": {"param_value": "190", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "QacEdelta1 is a resistance gene conferring resistance to antiseptics. It is different from QacE only at the 3'-terminus.", "model_sequences": {"sequence": {"6045": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTATGCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAATTGCTGCCTTTTTGCTCGCCCGATCCCCATCGTGGAAGTCGCTGCGGAGGCCGACGCCATGGTGA", "fmax": "1838", "accession": "U49101.1", "fmin": "1490", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AAC44316.1", "sequence": "MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVLKSIPVGVAYAVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSPSWKSLRRPTPW"}}}}, "ARO_category": {"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."}, "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": "qacEdelta1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43198", "model_name": "qacEdelta1", "model_type_id": "40292"}, "3825": {"model_id": "3825", "ARO_accession": "3005091", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "RanA is a part of the RanARanB ABC-type efflux system. Alongside RanB, it confers resistance to aminoglycoside antibiotics.", "model_sequences": {"sequence": {"6125": {"dna_sequence": {"partial": "0", "sequence": "ATGATTGAAGTTAAAGATTTAAGAAAAAGTTTTAATGATGTAGAGGTTCTCAAAGGAATTACTACTACTTTTGAAACAGGAAAAATAAACCTTGTCATTGGTCAATCGGGTTCTGGTAAAACAGTGTTTTTGAAGTGTTTACTCAATGTTTTTGACCCTTCTTCAGGAGATATTTTATTTGATGGAAGAAATCTAAGCATTATGGGGCGAACGGAAAAACAAGAAATTCGTTCTGAGATAGGCACGGTATTTCAAGGGAGTGCTTTATTTGACTCTATGACGGTAGAAGAAAATATATCTTTTCCTTTGGATATGTTTACCAATCTCACTTATACCGAAAAAAGAAAAAGAGTAAAAGAAGTAATTGGAAGAGTTCATTTAGAAAATGCTAACACCAAGTTTCCTTCTGAAATATCAGGCGGAATGCAAAAAAGAGTGGCAATAGCTCGTGCAATTGTGAACAATCCAAAATATCTCTTTTGTGACGAACCAAATTCTGGTTTAGACCCTAACACAGCCATTGTAATAGATGAGCTTATAAAAGAAATTACAGAGGAATATAATACTACGACGATTATCAACACCCACGATATGAACTCTGTACTTACTATAGGTGAGAAAATAGTTTATTTAAGAAAAGGTGTTAAAGAGTGGGAAGGTAACAAAGACCTTATTATCAAAGCAGAAAATGAGCATTTAATAGATTTTGTTTACTCTTCAGCTTTGTTTAAGCAAGTAAGGGAAACAATGTTAAGAAATAATCAAACTAATTTATAA", "fmax": "1618245", "accession": "CP002562.1", "fmin": "1617468", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Riemerella anatipestifer RA-GD", "NCBI_taxonomy_id": "992406", "NCBI_taxonomy_cvterm_id": "43303"}, "protein_sequence": {"accession": "ADZ12699.1", "sequence": "MIEVKDLRKSFNDVEVLKGITTTFETGKINLVIGQSGSGKTVFLKCLLNVFDPSSGDILFDGRNLSIMGRTEKQEIRSEIGTVFQGSALFDSMTVEENISFPLDMFTNLTYTEKRKRVKEVIGRVHLENANTKFPSEISGGMQKRVAIARAIVNNPKYLFCDEPNSGLDPNTAIVIDELIKEITEEYNTTTIINTHDMNSVLTIGEKIVYLRKGVKEWEGNKDLIIKAENEHLIDFVYSSALFKQVRETMLRNNQTNL"}}}}, "ARO_category": {"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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "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": "RanA", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43304", "model_name": "RanA", "model_type_id": "40292"}, "3757": {"model_id": "3757", "ARO_accession": "3005013", "model_param": {"blastp_bit_score": {"param_value": "775", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "blaIDC-1 is an IDC class C beta-lactamase and an integron cephalosprinase", "model_sequences": {"sequence": {"6047": {"dna_sequence": {"partial": "0", "sequence": "ATGCCGAGAACTGAATCCGTGCCATCCAAGTCCCTTGTCGTTAGGACGCTGCTGCTCGTCTTCGCTTGCCTCTTTCCTATGGCAGTTCCAGCCGTCGAAGACACCTCCCGTGTCCGCACCACCGTCGACGCCGCGATCCTGCCCCTAATGTCCCAGCATGACATCCCCGGCATGGTTGTCGGGCTGATCCTCGATGGCCAGCCCTATGTTGTTACGTATGGCGTCGCCTCGAAGGAAGCCAACGTACCGGTAGCGGAGGCAACACTATTCGAGATCGGCTCCGTCAGCAAAGTCTTCACCGCAACGCTGGCCGCCTACGCGCAAACCACCGGCAAACTCTCCCTGGACGACCATCCGGGCAAGTACCTGCCGCAGTTGAAGGGCACGCCGATCGACCAAGCCACGTTGCTCCACTTGGGAACCTACACCGCCGGCGGACTGCCGTTGCAGTTCCCTGATGAGGTGACGGGAGAGGTGGCGGTGATGGACTACTTCCGCAACTGGACGCCGCTAGCTCCCCCGGGCACACGGCGCGAGTACTCCAACGCGAGCCCGGGCTTGCTCGGGCTTGTTGCGGCCAGCGCGCTGGATGACGATTTCGCGACGTTGATGCAATCGACGGTATTTCCAGCGTTCGGCATGACGGACAGCTTCATTCACGTGCCGGACCGCAAGATGCCGGACTACGCGTGGGGCTATCGCAAGGACAGACCGGTCCGTGTGAACGAGGGGCCGCTCGACGAGCAGGCTTACGGTGTCAAGACGACGGTGTCGGACTTGCTCCGCTTCGTGCAAGCAAACATCGATCCGAGTTCGCTCGAGCCGTCGATGCGCCGCGCCGTCGAAGCCACGCAGGTCGGATACTTCCGCGCGGGGACTCTGGTGCAGGGCCTTGGGTGGGAAAAGTATCCGTACCCTGTCTCACGCGAATGGCTGCTCGGTGGCAACGCCAAGGAGATGCTTTTCGATCCACAGCCTGCCTATCGGCTGACGGACCAAACCGCGGGCGAGCGGTATCTCTTTAACAAGACGGGATCGACCGGCGGCTTCGCCACTTACGTGGCGTTCGTGCCCGCTAGGAAGATCGGGATCGTCATGCTGGCAAACCGGAGTTATCCAATTCCGGATCGCGTTGAGGCCGCCTGGATCATTCTGGAACAACTTGCATCAGGGACCGACTCAAACTGA", "fmax": "1531", "accession": "MN985646.1", "fmin": "343", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "sediment metagenome", "NCBI_taxonomy_id": "749907", "NCBI_taxonomy_cvterm_id": "43201"}, "protein_sequence": {"accession": "QIB98910.1", "sequence": "MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDTSRVRTTVDAAILPLMSQHDIPGMVVGLILDGQPYVVTYGVASKEANVPVAEATLFEIGSVSKVFTATLAAYAQTTGKLSLDDHPGKYLPQLKGTPIDQATLLHLGTYTAGGLPLQFPDEVTGEVAVMDYFRNWTPLAPPGTRREYSNASPGLLGLVAASALDDDFATLMQSTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRPVRVNEGPLDEQAYGVKTTVSDLLRFVQANIDPSSLEPSMRRAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEMLFDPQPAYRLTDQTAGERYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWIILEQLASGTDSN"}}}}, "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."}, "43199": {"category_aro_name": "IDC beta-lactamase", "category_aro_cvterm_id": "43199", "category_aro_accession": "3005011", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "IDC beta-lactamases are class C beta-lactamases inc. cephalosporinases and carbapenemases."}}, "ARO_name": "IDC-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43202", "model_name": "IDC-2", "model_type_id": "40292"}, "3828": {"model_id": "3828", "ARO_accession": "3005096", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GPC-1 is a class A beta-lactamase. It is part of the GPC beta-lactamase gene family. Originally found in Pseudomonas aeruginosa. Confers resistance to B-lactams.", "model_sequences": {"sequence": {"6128": {"dna_sequence": {"partial": "0", "sequence": "ATGACGATAACCATTTCACGCCGCCAGGCCATGGCCGGCGCTCTTCTTGCCATTCCCGCGGTTTCTGCGCTGACGGCCGGCACCAGCCGCGCCGCCGGTGAGAACCTTGCGCAACGGCTTGCCGCATTAGAGGCACGCCACGGCGGGCGCATCGGCGTTGCAATACATAATCTTTCGACAGGCGCGCGGCTCGGTCACAACACGGACGAGCGTTTCCTGATGTGCAGCACCTTCAAGGCGCTGCTGGCGGGCCATATCCTCGTCCGGGTGGACCGCGGCGAGGAGACGCTGGACCGACGCATCGTCGTGAAGGAAGCGGATCTCGTGGATTGGTCGCCGGTGGTGGAAAAGCGCATCGGCGGGGATGTCATCTCTATTGCCGAACTCTGCGAGGCGACCATCACGCTCAGCGACAATGCCGCCGCCAACCTGCTGCTCGCCGCATCGGGCGGGCCTAAGGCCGTCACGGCGTTTCTGCGTGGCCTCGGCGATGAAGTGACGCGTCTCGACCGTACGGAGCCGACGCTCAACTACCACGAGACGCCGGGCGATGAGCGTGACACGACGACGCCGAGCGCCATGGTGGAGACGCTGCGCAGGCTGCTCTTCACGGACGTTCTGTCGGCGCGTTCGAAGGCGCAGCTTGCCGCCTGGCTGATAATGAACAAGACGGGCGACACGCGGCTGCGCGCTGGCTTCCCGGCAGACTGGATGACCGGCGACAAGACCGGCACCAACGGCGACAAGGCCGGAAACGCCAACGATGTCGCGGTCGCCTGGTCGCCGGATCGCGGTGCAGTCATTGTTGCCGCCTTCTGCGAAATCCCCGGCATTTCCGGTGACGAGCGCAATGCCGTTATTGCCGAAATCGGGCGCATCGCGGCAGAGGTCTGA", "fmax": "894", "accession": "MH211206.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AWB15813.1", "sequence": "MTITISRRQAMAGALLAIPAVSALTAGTSRAAGENLAQRLAALEARHGGRIGVAIHNLSTGARLGHNTDERFLMCSTFKALLAGHILVRVDRGEETLDRRIVVKEADLVDWSPVVEKRIGGDVISIAELCEATITLSDNAAANLLLAASGGPKAVTAFLRGLGDEVTRLDRTEPTLNYHETPGDERDTTTPSAMVETLRRLLFTDVLSARSKAQLAAWLIMNKTGDTRLRAGFPADWMTGDKTGTNGDKAGNANDVAVAWSPDRGAVIVAAFCEIPGISGDERNAVIAEIGRIAAEV"}}}}, "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."}, "43308": {"category_aro_name": "GPC beta-lactamase", "category_aro_cvterm_id": "43308", "category_aro_accession": "3005095", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "GPC is a class A beta-lactamase family. It is found initially in Pseudomonas aeruginosa. It confers resistance to B-lactams."}}, "ARO_name": "GPC-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43309", "model_name": "GPC-1", "model_type_id": "40292"}, "3815": {"model_id": "3815", "ARO_accession": "3005078", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-8 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.", "model_sequences": {"sequence": {"6110": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTCTGTTCCTTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTCGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "1118", "accession": "KJ910996.1", "fmin": "200", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AIW80573.1", "sequence": "MLNKLKIGTLLLLTLTACLPNSVPSVTSNPQPASAPVQQSATQATFQQTSANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-8", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43285", "model_name": "ROB-8", "model_type_id": "40292"}, "3824": {"model_id": "3824", "ARO_accession": "3005090", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "RanB is the determinant of antibiotic resistance within the RanARanB ABC-type efflux system. It confers resistance to aminoglycoside antibiotics.", "model_sequences": {"sequence": {"6124": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAAGTTGTCAAAAAGAATGCTTACCTCTGTGGGAGAGTATGTTTTGTTACTAGGAAAAGTAATAAAACGCCCGCAGAAGCATAATATTTTTTTTAAACTCTTGATGAGAGAGATTAACGATTTAGGCGTTAACTCCTTTGGTTTGGTCTTATTTACTTCCATATTTGTGGGAGCTGTAGTCGCAATACAAATGTATAATAACTTTAAGGCTTCTACCATTCCCATTCCACTGTACTTCATAGGTTATGCTACTAAGGTGGTGCTTATTTTAGAGTTTTCGCCTACTATCATTAGTCTTATTTTGGCAGGTAAAGTAGGGTCTTACATCGCGTCTAGTATAGGAACGATGAGAGTGACGGAGCAGATAGACGCTTTAGATATTATGGGTGTTAATTCCCCCAACTTTTTGATTCTTCCAAAGATAGTAGCTAATGTTATTTTTAATCCGTTACTCATAGCCATTAGTATTGTTTTCGGTATTTATGGAGGTTATTTAGCAGGAGTTGCCACGGGCAATTGGACAGAAGCCGACTATATTACAGGGATACAAAGATATATTCCAGACTACTTTATATGGTATGCTTTTTTTAAAACGGTGGTGTTTGCGTTCCTTATTGCTACAATTCCAGCTTATTTTGGTTATAATGTAAAGGGAGGCTCTTTAGAAGTAGGTAGAGCTAGCACCCAAGCAGTAGTTTGGACTATGGTGGCAATTATTATTGCCGAACTTATATCAACCCAATTATTTTTAAGCTAA", "fmax": "1619006", "accession": "CP002562.1", "fmin": "1618244", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Riemerella anatipestifer RA-GD", "NCBI_taxonomy_id": "992406", "NCBI_taxonomy_cvterm_id": "43303"}, "protein_sequence": {"accession": "ADZ12700.1", "sequence": "MLKLSKRMLTSVGEYVLLLGKVIKRPQKHNIFFKLLMREINDLGVNSFGLVLFTSIFVGAVVAIQMYNNFKASTIPIPLYFIGYATKVVLILEFSPTIISLILAGKVGSYIASSIGTMRVTEQIDALDIMGVNSPNFLILPKIVANVIFNPLLIAISIVFGIYGGYLAGVATGNWTEADYITGIQRYIPDYFIWYAFFKTVVFAFLIATIPAYFGYNVKGGSLEVGRASTQAVVWTMVAIIIAELISTQLFLS"}}}}, "ARO_category": {"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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "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": "RanB", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43302", "model_name": "RanB", "model_type_id": "40292"}, "3811": {"model_id": "3811", "ARO_accession": "3005075", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-5 is a class A beta-lactamase from the blaROB AMR gene family. It was found in Moraxella sp. RCAD0137.", "model_sequences": {"sequence": {"6106": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACACCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "11919", "accession": "LTCC01000022.1", "fmin": "11001", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella sp. RCAD0137", "NCBI_taxonomy_id": "1775913", "NCBI_taxonomy_cvterm_id": "43282"}, "protein_sequence": {"accession": "PNP96721.1", "sequence": "MFNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNTATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43281", "model_name": "ROB-5", "model_type_id": "40292"}, "3823": {"model_id": "3823", "ARO_accession": "3005089", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "mef(D) is a major facilitator superfamily efflux pump protein. It works together with the msr proteins to confer resistance to macrolide antibiotics.", "model_sequences": {"sequence": {"6123": {"dna_sequence": {"partial": "0", "sequence": "GTGAAAAATAATAAATGGAAAAAGAAATTTATAGCAATATATATAGGGCAGTTCTTTTCTTTATTAAGTAGTGCTGCTGTACAATTCAGTATCATTTGGTGGTTAACAGATAAAACAGGAGGATCACCTCTTGTACTGACATTAGCAGGTCTTGCCGGTTTTTTACCACAAGCATTAGCAGGGCCATTTGCTGGAACAATTACGGATCGTTATTCAAGAAAATTAATGATGATTCTAGCAGATATGACAGTTGCATTGGGAAGTTTAATCTTATTTATTTCATTGTATTTTTATGAAATAAATATTTCATTTGTAATTTTAATATTAGCAATTCGCTCATTAGCAACGGCATTTCATATGCCTGCCCTGCAAGCATCTATTCCATTGCTTGTTCCTGAAGATGATCTTACTAAGGCCGCTGGATGGGGACAGACAGTAAGTTCTATATCAAATATAACAGGTCCCGCTGTAGGTATGTCAATACTTGCTGCAAGTTCTATAGAATGGGTTTTATTACTTGATGTTTTGGGAGCAGTGATAGCAAGTGGTATTTTACTATTCATTTACATTCCTAAAATTCAAAATCAAAATCAACAATCGATAGATTCTAAAGGGTTTTTTATTGAAATGAAGGATGGATATAACGCGCTTGTCAATCATCCAATCTTATTAAAACTAACGTTTGTTATGACATCTGTTGCAGTTTTATACATTCCGCTAGGTACTTATTTTCCTCTTATAACAAGGAATCACTTTAATAAGGGAGTTGTTGAAGCTGGAATCGTAGAGATTATTTTTGCTGTTGGACTAATTATTGGTGGTTCGTTCCTGGGAATACTTGGAGATAAATTTAATAAAATTAATACAATGACAACTGGAATATTGTTGATGGGAATTGCGTTATTTTTAACGGGTATTCTATCACCTTCTCTTTTCTATTTCTTTGTTGTTTTAGCTGGTTTAGTAGGATTTTCTGGGCCTTTATTTTCAGCACCGTTTTATGCATTAATCCAATCTGAAATTGAGCCTCATCTTTTAGGAAGAGTTTTTAGTTTCGTTACTAGTATCTCGTTATTAGCAACACCATTAGGATATGTTATTGCAGGATTATTGATAGAGATAACGAATGTATCTACACTATTTTCTATAATTGGAGTGTTGATTATTTTCAATGGAATTATTATTAATAGATTGAAGTAG", "fmax": "18658", "accession": "MN728681.1", "fmin": "17458", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Macrococcus canis", "NCBI_taxonomy_id": "1855823", "NCBI_taxonomy_cvterm_id": "43299"}, "protein_sequence": {"accession": "QHW12307.1", "sequence": "MKNNKWKKKFIAIYIGQFFSLLSSAAVQFSIIWWLTDKTGGSPLVLTLAGLAGFLPQALAGPFAGTITDRYSRKLMMILADMTVALGSLILFISLYFYEINISFVILILAIRSLATAFHMPALQASIPLLVPEDDLTKAAGWGQTVSSISNITGPAVGMSILAASSIEWVLLLDVLGAVIASGILLFIYIPKIQNQNQQSIDSKGFFIEMKDGYNALVNHPILLKLTFVMTSVAVLYIPLGTYFPLITRNHFNKGVVEAGIVEIIFAVGLIIGGSFLGILGDKFNKINTMTTGILLMGIALFLTGILSPSLFYFFVVLAGLVGFSGPLFSAPFYALIQSEIEPHLLGRVFSFVTSISLLATPLGYVIAGLLIEITNVSTLFSIIGVLIIFNGIIINRLK"}}}}, "ARO_category": {"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."}, "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": "mef(D)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43301", "model_name": "mef(D)", "model_type_id": "40292"}, "3822": {"model_id": "3822", "ARO_accession": "3005088", "model_param": {"blastp_bit_score": {"param_value": "900", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "msrH is a ABC-F binding cassette ribosomal protection protein. It confers resistance to macrolide antibiotics.", "model_sequences": {"sequence": {"6122": {"dna_sequence": {"partial": "0", "sequence": "ATGGAACAAATATGTTTTGAATTAGAGAATATTGAATTAAGTTATTTAGATAAAAAAGTGTTGGATATTGATCGATTAGCTATTCATCAGTTTGATAGAATAGGTATTGTGGGAAGAAATGGAGCAGGAAAAAGTACATTATTGAAAATAATTGGTGGTATTATTAATCCTTCTAGAGGAAAGGTTAATCAATATGTAGAGTACGGGTATTTCGAACAATTAGAAGGTCCGATAGCTAAAGCAACTAATCCGCGCTTATTAGGTAAGTTGCAAGTAAAAGAGAACGCTAGTAATTTAAGTGGTGGTGAACAGACAAGGCTCAAACTTGCGCAATTATTTACCCATTTTTATGATGCGTTGTTAATTGATGAGCCTACAACACATTTGGATCAAGATGGTATCTCATTTCTTATCGAAGAACTTAAGAATTATTATGGTGCTTTAATTTTAATAAGTCATGATCGTGCATTTCTGGATGAACTTGTTACAACAATATGGGAAATTGATGAAGGTACAGTTAAAATATATTCTGGAAATTATAGTGATTATATGAGGCAGAAGCAAATAGAAAGAACGCAACAAGTTTACAATCATGAACAATTTTTGAAAGAAAAGAATAGGCTTGAAAAAGCATCACTAGAAAAAATGAAAAAAGCTGAAAAAATTGCTAAATCTACTTCGATGTCAAAGAAAGAGTCTAAGGCAAAGCCAAATCGTATGTTCGAATCAAAGTCGAAAGGCACAAGTCAGAAATCGTTACAACGTGCTGCAAAAGCAATCGAGCAAAGAATAAACCAACTGCAAGTTGTAGAAGCACCAAATGATGATTACGTCATTCATTTCCATTCGACTAATAATATATCAAAATTGCATAATAAATTTCCGATTATGGGGGATTGTATAACGCTAGAGATAGATGATAAAGTACTATTAAAAGAAACAAGTTTTCAATTTCCTTTAGGTAAAACAATAGCAATTACTGGTAAGAATGGTTCAGGTAAAACAACATTGATTCGTCATATTATTGAAAATGGTGAGGGTATCACTATTTCCCCAAAAGCAGAGATTGGAATATATGAACAAATGGGTTATCAGTTCGATGAAGATAAAACTGTTTTATCGTATATAAAAGATAGAAGTGATTATGATGAAAGTAAAATACGTTCTGTTCTTAATGCGATGAGTTTTACTGGTAATGACTTGAAGAAGAAAGTTCAAAACTTAAGTGGAGGAGAATCAATACGGTTAGTATTATGTCAACTTTTTTTAGGAAGGTATAATATTTTAGTTCTAGATGAGCCAACAAACTTTTTAGATATTTTTTGTATTGAAGCATTAGAGAGTATTTTAAAAGAATACAAAGGTACTGTAATTATTATTTCACATGATAAAAAATTTGTTGAACATGTTTCTGATATAGTTTATAGAATAGAAAACCAAAAATTGAAATTAGTAAATTGA", "fmax": "26977", "accession": "BK011995.1", "fmin": "25516", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Macrococcus canis", "NCBI_taxonomy_id": "1855823", "NCBI_taxonomy_cvterm_id": "43299"}, "protein_sequence": {"accession": "DAC81085.1", "sequence": "MEQICFELENIELSYLDKKVLDIDRLAIHQFDRIGIVGRNGAGKSTLLKIIGGIINPSRGKVNQYVEYGYFEQLEGPIAKATNPRLLGKLQVKENASNLSGGEQTRLKLAQLFTHFYDALLIDEPTTHLDQDGISFLIEELKNYYGALILISHDRAFLDELVTTIWEIDEGTVKIYSGNYSDYMRQKQIERTQQVYNHEQFLKEKNRLEKASLEKMKKAEKIAKSTSMSKKESKAKPNRMFESKSKGTSQKSLQRAAKAIEQRINQLQVVEAPNDDYVIHFHSTNNISKLHNKFPIMGDCITLEIDDKVLLKETSFQFPLGKTIAITGKNGSGKTTLIRHIIENGEGITISPKAEIGIYEQMGYQFDEDKTVLSYIKDRSDYDESKIRSVLNAMSFTGNDLKKKVQNLSGGESIRLVLCQLFLGRYNILVLDEPTNFLDIFCIEALESILKEYKGTVIIISHDKKFVEHVSDIVYRIENQKLKLVN"}}}}, "ARO_category": {"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."}, "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."}, "41687": {"category_aro_name": "ABC-F ATP-binding cassette ribosomal protection protein", "category_aro_cvterm_id": "41687", "category_aro_accession": "3004469", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A subfamily of the ATP-binding cassette protein superfamily. Unlike other ABC proteins, ABC-F genes are not fused to a transmembrane domain nor associated with transport. It has been shown that ABC-F proteins confer antibiotic resistance via ribosomal protection and not antibiotic efflux as in other ABC proteins."}, "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."}, "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."}, "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."}, "36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}, "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."}, "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": "msrH", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43300", "model_name": "msrH", "model_type_id": "40292"}, "3799": {"model_id": "3799", "ARO_accession": "3005059", "model_param": {"blastp_bit_score": {"param_value": "1500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LptD is involved in LPS transport in a ABC Transporter efflux system. It confers resistance to carbapenems, rifamycin, aminocoumarin and peptide antibiotics.", "model_sequences": {"sequence": {"6094": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAACGTATTCCCAGCCTCCTGGCTACGATGATTGCCAGCGCCTTGTATAGCCAACAAGGCCTCGCTGCCGATCTCGCAACGCAATGTATGCTTGGCGTGCCAAGCTATGATCGTCCGCTCGTGGAAGGTCGTCCTGGCGATCTGCCGGTGACGATTAACGCCGATCATGCGAAGGGCAACTACCCGGACAACGCCGTCTTTACCGGCAACGTCGATATTAACCAGGGGAATAGTCGCCTCCGCGCCGACGAAGTTCAGCTGCACCAGCAGCAGGCCGCGGGCCAGGCGCAGCCGGTGCGCACGGTGGACGCGCTGGGCAACGTGCATTACGACGATAACCAGGTGATCCTCAAAGGGCCAAAAGCCTGGTCGAATCTGAATACCAAAGATACCAACGTCTGGCAGGGCGATTATCAAATGGTCGGACGCCAGGGACGCGGCACCGCCGACCTGATGAAACAGCGCGGTGAAAACCGCTATACCATTCTCGAAAACGGCAGCTTTACCTCCTGTCTGCCGGGCTCCGACACCTGGAGCGTCGTCGGCAGCGAAGTTATCCACGATCGCGAAGAGCAGGTTGCCGAGATCTGGAACGCCCGCTTCAAGCTTGGCTCTGTGCCGATTTTCTATAGCCCCTACCTGCAGCTGCCGGTGGGCGATAAGCGTCGTTCAGGCTTCCTGATCCCGAACGCGAAATACAGCACCAAAAACGGCGTGGAATTCTCCCTGCCGTACTACTGGAACATCGCGCCAAACTTCGATGCCACCATTACTCCGCACTATATGAACAAACGCGGCGGCGTGATGTGGGAAAACGAGTTCCGCTATCTGACCCAGCTCGGCAGCGGCTTAACTGAATTCGACTACCTGCCGTCGGATAAAGTCTACGAAGACGACCACTCGAGCGACAGCAACAGCCGCCGCTGGCTGTTCTACTGGAACCACTCAGGGGTTATCGATCAGGTATGGCGTCTGAACGCTGACTACACCAAGGTCAGCGATCCTGACTACTTCAACGACTTCAGCTCGAAATATGGTTCCAGTACCGATGGCTATGCGACGCAGAAATTCAGCGCCGGTTACGTCAACCAGAACTTTGACGCCACGGTATCGACCAAACAGTTCCAGGTCTTTGACCGCGAATCGAGCAACTCCTATTCGGCTGAGCCGCAGCTCGACGTCAACTACTACCAGAATGATGTCGGTCCGTTCGATACCCATCTCTATGGACAGGTTGCCCATTTTGTTAACTCGAATAACAACATGCCGGAAGCGACCCGCGTTCACTTCGAACCGACGATCAACCTGCCGCTGTCCAACGGTTGGGGCAGTCTGAATACCGAAGCCAAGCTGCTGGCGACTCACTACCAGCAGAGCAACCTCGATAAGTACAATGCCGCCAACGGCACTGACTATAAAGAGTCCGTCAGCCGCGTAATGCCGCAGTTTAAAGTCGACGGCAAAATGGTCTTTGAACGCGACCTGCAGGAGGGATTCACCCAAACGCTGGAACCGCGCGTGCAGTATCTGTACGTGCCGTACCGCGATCAGAGTGAAATCGGCAACTACGACTCCACGCTGTTGCAGTCGGATTACACCGGTCTGTTCCGCGACCGTACCTATAGCGGTCTGGACCGCATCGCGTCGGCTAATCAGGTCACCACCGGGCTCACCTCGCGCGTGTATGATGCCGCCGCGGTGGAACGTTTTAATATTTCCGTTGGTCAAATCTACTATTTCACCGAGTCACGCACCGGTGATGACAACATCAACTGGGAGAACAACGATACCACGGGTTCACTGGTCTGGGCCGGCGATACCTACTGGCGCATTGCCGATGAATGGGGTCTGCGCGGAGGGATCCAGTACGATACGCGTCTGGATAACGTTGCCACTGGTAACGGCACCATTGAATACCGTCGCGATGAGAACCGCTTAGTTCAGCTTAACTATCGTTACGCCAGCCCGGAATATATTCAGGCCACGCTGCCGTCATATTCCACCGCGGCACAATATAAACAGGGTATTTCGCAGGTGGGGATGACCGCCAGTTGGCCGATTGTCGATCGCTGGTCCGTGGTCGGGGCCTACTACTACGATACTAATACCCGGAAAGCAGCAAACCAGATGTTGGGTGTGCAGTATAACTCCTGCTGCTACGCCATCCGTCTTGGCTACGAACGTAAAGTCAACGGCTGGAACAGCAACGACAACGGCGGCGAGAGCAAATACGATAACACCTTCGGAATCAATATCGAATTGCGCGGTCTGAGCTCTAACTACGGCCTCGGCACCCAGCAGATGCTGCGCTCGAACATTTTACCGTACCAGAGCTCCCTGTGA", "fmax": "809555", "accession": "CP007727.1", "fmin": "807206", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae subsp. pneumoniae KPNIH10", "NCBI_taxonomy_id": "1094170", "NCBI_taxonomy_cvterm_id": "43262"}, "protein_sequence": {"accession": "AIA35096.1", "sequence": "MKKRIPSLLATMIASALYSQQGLAADLATQCMLGVPSYDRPLVEGRPGDLPVTINADHAKGNYPDNAVFTGNVDINQGNSRLRADEVQLHQQQAAGQAQPVRTVDALGNVHYDDNQVILKGPKAWSNLNTKDTNVWQGDYQMVGRQGRGTADLMKQRGENRYTILENGSFTSCLPGSDTWSVVGSEVIHDREEQVAEIWNARFKLGSVPIFYSPYLQLPVGDKRRSGFLIPNAKYSTKNGVEFSLPYYWNIAPNFDATITPHYMNKRGGVMWENEFRYLTQLGSGLTEFDYLPSDKVYEDDHSSDSNSRRWLFYWNHSGVIDQVWRLNADYTKVSDPDYFNDFSSKYGSSTDGYATQKFSAGYVNQNFDATVSTKQFQVFDRESSNSYSAEPQLDVNYYQNDVGPFDTHLYGQVAHFVNSNNNMPEATRVHFEPTINLPLSNGWGSLNTEAKLLATHYQQSNLDKYNAANGTDYKESVSRVMPQFKVDGKMVFERDLQEGFTQTLEPRVQYLYVPYRDQSEIGNYDSTLLQSDYTGLFRDRTYSGLDRIASANQVTTGLTSRVYDAAAVERFNISVGQIYYFTESRTGDDNINWENNDTTGSLVWAGDTYWRIADEWGLRGGIQYDTRLDNVATGNGTIEYRRDENRLVQLNYRYASPEYIQATLPSYSTAAQYKQGISQVGMTASWPIVDRWSVVGAYYYDTNTRKAANQMLGVQYNSCCYAIRLGYERKVNGWNSNDNGGESKYDNTFGINIELRGLSSNYGLGTQQMLRSNILPYQSSL"}}}}, "ARO_category": {"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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "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": "LptD", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43261", "model_name": "LptD", "model_type_id": "40292"}, "3821": {"model_id": "3821", "ARO_accession": "3005087", "model_param": {"blastp_bit_score": {"param_value": "900", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "msrF is an ABC-F binding cassette ribosomal protection protein. It confers resistance to macrolide antibiotics.", "model_sequences": {"sequence": {"6121": {"dna_sequence": {"partial": "0", "sequence": "ATGGAACAAATATGTTTTGAATTAGAAAATGTTGAAGTAACTTTTTTAGATAAAAAAATATTGGAGATTGATCGCTTAGCTGTTCATCAGTTTGATCGAATAGGTATTGTTGGAAAAAATGGGGCAGGAAAAAGTACATTATTGAAAATACTTGGTGGTATTATTAAGCCTACTAGAGGAAAAGTAAATCGTTATATAGATTACGGATATTTTGAACAAGTAGAAAGTCCTAAAGTCAGTATGGCTGATCCACGCTTATTAGGAAAATTAAATGTAAAAGTAGATTCAAATAATCTAAGTGGTGGTGAACTAACAAGACTGAAAATTGCTCAATTATTTACAGACTATTATGAATCGTTGTTAATTGATGAGCCTACGACACATTTAGATCAAGATGGAATTTCATTTCTCATAGATAAATTAAAGTATTATTATGGTGCATTAGTTTTAATCAGTCATGACCGCAATCTACTAGATGAACTCGTTACTACTATATGGGAAATTGATGATGGTATGATTAAAGTATATTCTGGAAATTACAGTGAGTATTTGAGACAGAAGAAGGTGGAAAGAGAGCAACAAGCGCATGATTTCGATCTATATTTGAAAGAAAAGAATAGGCTTGAAAAAGCAGCTAAGGAAAAAATGAATAAAGCTGAAAAAATTGCCAATTCGTCTTCAATGTCAAAGAAAGAATCCAAAGCAAAGGCAAACCGTATGTTTGAATCAAAATCAAAAGGTACAAGTCAGAAATCACTACAACGAGCTGCAAAAGCTGTTGAAAAAAGAATAGAGCAACTTGAAGTAGTGGATGCACCTAAAGAAATTCACACAATTCAATTTCATCAGACTCACTCCACACCACCATTACACAACAAGTTTCCAATATTGGGAGATCGTTTAACTCTACAAGCAGGGGATAAAACACTCTTAGAAGAAACGAGTTTTCAATTTCCATTAGGAAAAACTATAGCAATTACAGGTAATAATGGTTCTGGTAAAACGACATTGATTCATCATATTATTCAAAAGGGTGAAGGTATTACTATATCTCCTAAAGCTGTGATTGGATTTTATGAACAAATGGGATATCAGTTCAATGAAGATAAAACTGTATTATCTTATATGAAAGCTAGAAGTGATTATGATGAAAGTAAAATACGTTCAGTTTTACACGCTATGAATTTCAATGGTAATGACTTGAAAAAGAATGTACGATATTTAAGTGGAGGAGAAGCAACTCGATTAGTATTATGTCAGCTTTTTTTAGGAAGATATAATATTTTGATTCTAGATGAGCCAACAAACTTTTTAGACATTTTTTGTATAGAAGCATTAGAGAGATTTATAGAAGAATATGAAGGGACTATTATTCTTATTTCGCATGATAAGAAGTTTGTAGATCATGTATCTGATACTATTTATAAAATAGAAAATAAAAAGTTGAATTTGGTAAATTAA", "fmax": "18847", "accession": "MN728682.1", "fmin": "17386", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Macrococcus canis", "NCBI_taxonomy_id": "1855823", "NCBI_taxonomy_cvterm_id": "43299"}, "protein_sequence": {"accession": "QHW12375.1", "sequence": "MEQICFELENVEVTFLDKKILEIDRLAVHQFDRIGIVGKNGAGKSTLLKILGGIIKPTRGKVNRYIDYGYFEQVESPKVSMADPRLLGKLNVKVDSNNLSGGELTRLKIAQLFTDYYESLLIDEPTTHLDQDGISFLIDKLKYYYGALVLISHDRNLLDELVTTIWEIDDGMIKVYSGNYSEYLRQKKVEREQQAHDFDLYLKEKNRLEKAAKEKMNKAEKIANSSSMSKKESKAKANRMFESKSKGTSQKSLQRAAKAVEKRIEQLEVVDAPKEIHTIQFHQTHSTPPLHNKFPILGDRLTLQAGDKTLLEETSFQFPLGKTIAITGNNGSGKTTLIHHIIQKGEGITISPKAVIGFYEQMGYQFNEDKTVLSYMKARSDYDESKIRSVLHAMNFNGNDLKKNVRYLSGGEATRLVLCQLFLGRYNILILDEPTNFLDIFCIEALERFIEEYEGTIILISHDKKFVDHVSDTIYKIENKKLNLVN"}}}}, "ARO_category": {"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."}, "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."}, "41687": {"category_aro_name": "ABC-F ATP-binding cassette ribosomal protection protein", "category_aro_cvterm_id": "41687", "category_aro_accession": "3004469", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A subfamily of the ATP-binding cassette protein superfamily. Unlike other ABC proteins, ABC-F genes are not fused to a transmembrane domain nor associated with transport. It has been shown that ABC-F proteins confer antibiotic resistance via ribosomal protection and not antibiotic efflux as in other ABC proteins."}, "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."}, "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."}, "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."}, "36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}, "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."}, "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": "msrF", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43298", "model_name": "msrF", "model_type_id": "40292"}, "3760": {"model_id": "3760", "ARO_accession": "3005016", "model_param": {"blastp_bit_score": {"param_value": "782", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CMY-150 is a CMY-2 variant differing by 15 amino-acid substitutions. It confers higher resistance levels to ceftazidime and aztreonam compared to CMY-2.", "model_sequences": {"sequence": {"6050": {"dna_sequence": {"partial": "1", "sequence": "TGCTAAATTTAACCGTTTGTCAACACGGTGCAAATCAAACACACTGATTGCGTCTGACGGGCCCGGACACCCTTTTGCTTTTAATTACGGAACTGATTTCATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACATTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAACTGACAGAGGGGTCCGGTAAATCGGACCTCCTTTCTTGCTCTTTTTTCCCTGCTGTCATCTACACTTAACAAAAAACAGTAAGGAAAACACTATGCGCAT", "fmax": "21480", "accession": "QCWX01000028.1", "fmin": "20134", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter freundii", "NCBI_taxonomy_id": "546", "NCBI_taxonomy_cvterm_id": "36915"}, "protein_sequence": {"accession": "PUU64961.1", "sequence": "MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKHSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"}}}}, "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."}, "36208": {"category_aro_name": "CMY beta-lactamase", "category_aro_cvterm_id": "36208", "category_aro_accession": "3000069", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins."}, "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."}}, "ARO_name": "CMY-150", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43207", "model_name": "CMY-150", "model_type_id": "40292"}, "3795": {"model_id": "3795", "ARO_accession": "3005053", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ArnT is involved in Cell Wall Biosynthesis, specifically 4-amino-4-deoxy-L-arabinose (Ara4N). It confers resistance to peptide antibiotics.", "model_sequences": {"sequence": {"6090": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAGCATTCGCTATGGCGTCTCTCTGATTGCGCTGTTTGCGCTGTATTATCTGCTGCCGCTCAATTTCCGTTTGCTCTGGCAACCCGACGAAACCCGCTACGCGGAGATCAGCCGTGAAATGCTGGCCACCGGCGACTGGGTGGTACCGCATTTTCTCGGCCTGCGCTACTTCGAAAAACCGATTGCCGGTTACTGGATCAACAGTATCGGTCAGTGGCTGTTTGGCCATAATAACTTCGGCGTACGCTTCGGGTCGGTCTTCGCCATCACCATGACCGCCCTGCTGGTGGCCTGGCTGGCGTGGCGGATCTTTCGTGATAAGCGGGTAGCTATCCTGTCGCTGATTATCTTCCTCACCGCGATGCTGGTGTATGCGATTGGCACCTATGCGGTGCTGGACCCGATGATCACCCTGTGGCTGGCGCTGGCGATGTGCAGCTTCTGGGGCGCGGTGCAGGCGCACAGCCGCAGCGGCAAAATACTGGGCTACGTGCTGCTGGGCGTCGCCTGCGGGATGGGGGTGATGACCAAGGGCTTCCTGGCGCTGGCGGTGCCGGTGGTGGGCGTTCTGCCGTGGGTGATCGCCCGTAAACGCTGGCGTGAAGTGCTGACCTACGGCTGGCTGGCGGTAATCGTCTGTACGCTGGTGGTGCTGCCCTGGGGGCTGGCTATCGCTCAGCGCGAGCCGGACTTCTGGCGCTACTTCTTCTGGGTCGAGCATATTCAGCGTTTTGCTGAAAAAGACGCCCAGCACAAAGCGCCGTTCTGGTACTACATCCCGTTCCTGATCGCCGGCAGTCTGCCGTGGCTGGCCCTGCTGCCGGGGGCGCTAAAGCGCGGCTGGCTTGAGCGCGATGAGGCCCGCGGCGCGCTGTATCTGTTAGGTTGGGTGGCGATGCCGTTCCTGTTCTTCAGTATCGCCAAAGGCAAACTGCCGACCTATATTCTGCCGTGCTTTGCGCCGCTGTCGATCCTGATGGCCCGCTACGCGCTGGAGGCCGCAAAGACCGGCGCGAAAGCGTTGCGCATCAACGGGATGATCAACCTGGGCGTTGGTTTGCTGGGGCTTATCGCCGTGCTGGTGGTCTCGCCGTGGGGCTTCATGCATAAGCCGGTGTGGACCAAGATTGAGCTGTATAAATGTCTGCTGGCGGCGATCGCTTTTGCCGTCTGGGCGCTGATGGGCTGGCTGGCGATGAAAGACTCTGGCCGCCGCTGGAGCCTCGCCGCGCTCTGTCCGCTCGGCCTGGCGCTGCTGGTGGGCTTCGCCATCCCGGACCGGGTTATCGACAGCAAACAGCCGCAGTTCCTCGTGGATATCGTCAGCGAATCCCTGCAGCCCAGCCGTTACGTCCTGACCAACAACGTTGGGATCGCCGGCGGCCTGGCCTGGGAGCTGAAGCGAAGCGATATTATTATGTTCGACAAACAGGGTGAGCTGAAGTACGGTCTCGACTGGCCGGATGCTCAGGGAAGCTTTGTCAGCCAGGCCGGTTTTGCCGACTGGCTGGCCGCGCATCGTCAGCAGGGGCCGGTCTCGCTGGTGCTGTTGATGGATAAAGGAGAGAGTATGCTCGACTTACCGTTACCGAAACCGGATAACGCCTACGAGCTGGGCCGGGTCGTTTTCCTTCAGTACCTGCCGCAATGA", "fmax": "306633", "accession": "FO834906.1", "fmin": "304977", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "CDO12042.1", "sequence": "MKSIRYGVSLIALFALYYLLPLNFRLLWQPDETRYAEISREMLATGDWVVPHFLGLRYFEKPIAGYWINSIGQWLFGHNNFGVRFGSVFAITMTALLVAWLAWRIFRDKRVAILSLIIFLTAMLVYAIGTYAVLDPMITLWLALAMCSFWGAVQAHSRSGKILGYVLLGVACGMGVMTKGFLALAVPVVGVLPWVIARKRWREVLTYGWLAVIVCTLVVLPWGLAIAQREPDFWRYFFWVEHIQRFAEKDAQHKAPFWYYIPFLIAGSLPWLALLPGALKRGWLERDEARGALYLLGWVAMPFLFFSIAKGKLPTYILPCFAPLSILMARYALEAAKTGAKALRINGMINLGVGLLGLIAVLVVSPWGFMHKPVWTKIELYKCLLAAIAFAVWALMGWLAMKDSGRRWSLAALCPLGLALLVGFAIPDRVIDSKQPQFLVDIVSESLQPSRYVLTNNVGIAGGLAWELKRSDIIMFDKQGELKYGLDWPDAQGSFVSQAGFADWLAAHRQQGPVSLVLLMDKGESMLDLPLPKPDNAYELGRVVFLQYLPQ"}}}}, "ARO_category": {"41433": {"category_aro_name": "pmr phosphoethanolamine transferase", "category_aro_cvterm_id": "41433", "category_aro_accession": "3004269", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane."}, "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."}, "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."}}, "ARO_name": "ArnT", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43254", "model_name": "ArnT", "model_type_id": "40292"}, "3794": {"model_id": "3794", "ARO_accession": "3005052", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LpsA plays a role in Lipooligosaccharide biosynthesis. LpsA confers resistance to polymyxin antibiotics.", "model_sequences": {"sequence": {"6089": {"dna_sequence": {"partial": "0", "sequence": "ATGCATAATGCAGCTCAGCACAATTATGTTATCAGTTTAACTACTGAACAAAAACGCCGAAAACATATTACCGAAGAATTCGGTAAGCAGAATATTCCTTTCGAATTTTTTGATGCTATTACGCCCGACATTATTGAAGAAACCGCTAAAAAATTTAATATTACATTAGATCGCTCTCCTAAAGCCAAGTTGTCGGATGGGGAAATTGGTTGTGCATTAAGCCATATTGTTTTATGGGATTTAGCATTAGAAAATAATTTAAACTATATCAATATCTTTGAAGATGATATTCATTTGGGGGAAAATGCCAAAGAATTATTAGAAATTGATTATATTTCTGATGATATTCATGTTTTAAAATTAGAAGCAAATGGCAAGATGTTCTTTAAACAACCAAAATCTGTAAAATGCGATAGAAATGTTTATCCCATGACGGTAAAGCAATCAGGATGTGCAGGATATACTGTTACAGCAAAAGGGGCTAAATATTTGCTTGAATTAGTAAAAAATAAACCACTTGACGTGGCGGTTGATTCACTTGTTTTTGAGGATTTTTTACATTTTAAAGATTATAAAATAGTACAACTTTCTCCTGGTATTTGCGTTCAAGATTTTGTGTTACATCCAGATAATCCTTTTGAAAGCAGTTTACAAGAAGGACGAGATAGAGTACACGGAAATCAACGCAAGTTCTCTATTTTAGAAAAAATAAAAAATGAATTTGGACGAGTAAAAATAAAAATGTTTGGAAAACAAGTTCCATTTAAATAA", "fmax": "771", "accession": "DQ647421.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Haemophilus influenzae", "NCBI_taxonomy_id": "727", "NCBI_taxonomy_cvterm_id": "36768"}, "protein_sequence": {"accession": "ABG48543.1", "sequence": "MHNAAQHNYVISLTTEQKRRKHITEEFGKQNIPFEFFDAITPDIIEETAKKFNITLDRSPKAKLSDGEIGCALSHIVLWDLALENNLNYINIFEDDIHLGENAKELLEIDYISDDIHVLKLEANGKMFFKQPKSVKCDRNVYPMTVKQSGCAGYTVTAKGAKYLLELVKNKPLDVAVDSLVFEDFLHFKDYKIVQLSPGICVQDFVLHPDNPFESSLQEGRDRVHGNQRKFSILEKIKNEFGRVKIKMFGKQVPFK"}}}}, "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."}, "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."}, "43251": {"category_aro_name": "Intrinsic peptide antibiotic resistant Lps", "category_aro_cvterm_id": "43251", "category_aro_accession": "3005050", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "lpsB is involved in lipopolysaccharide synthesis. It provides intrinsic resistance to colistin and other peptide antibiotics such as polymyxins."}}, "ARO_name": "LpsA", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43253", "model_name": "LpsA", "model_type_id": "40292"}, "3827": {"model_id": "3827", "ARO_accession": "3005094", "model_param": {"blastp_bit_score": {"param_value": "530", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-898 is a class D beta-lactamase from the OXA family. It confers resistance to B-lactams and was originally found in Ralstonia pikettii.", "model_sequences": {"sequence": {"6127": {"dna_sequence": {"partial": "0", "sequence": "ATGCTGTCTTGCTGCTCGAAGTCCTTCGCGTTCGCCTTGATGGCCTGCCTGCTGGCAACAAGCGCCGCCACTGCCCGCGCTGAGCTGGTCGTGCGTAACGACCTCAAGCGCGTGTTCGACGCCGCCGGCGTCTCAGGCACCTTCGTGCTGATGGACATCAGCGCCGACCGGACCTATGTCGTCGACCCGGCGCGGGCCGCGCGACGCATCCATCCGGCCTCCACCTTCAAGATCCCGAACAGTCTGATCGCCTTCGACACCGGCGCCGTGCGCGACGACCACGAAGTGCTGCCCTACGGCGGCAAGCCGCAACCCTTCAAGCAGTGGGAGCACGACATGGCATTGCCCGAAGCGATTCGCCTATCCGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTGGGTTTCGAGCGCATGCAGGCCTACGTCGATGCGTTTGACTACGGCAATCGCCAGCTCGGCGGCGTGATCGACCAGTTCTGGCTGCGTGGCCCGCTGGAGATTTCTGCACTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCCCGCACGTGGGACATGGTCCACCGCATGCTGTTGATCGAGCAGCAGGGCGACGCCGCGCTGTATGCCAAGACAGGCGTTGCCACGGAGTATCAGCCGGAGATCGGCTGGTGGGTCGGTTGGGTCGAGCGTGCCGGGCGCGTGTATGCCTTCGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCAGGCGCTGGAGGTGTGGCCGACGCTGTGA", "fmax": "816", "accession": "MN968728.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Ralstonia pickettii", "NCBI_taxonomy_id": "329", "NCBI_taxonomy_cvterm_id": "36921"}, "protein_sequence": {"accession": "QHT72948.1", "sequence": "MLSCCSKSFAFALMACLLATSAATARAELVVRNDLKRVFDAAGVSGTFVLMDISADRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPFKQWEHDMALPEAIRLSAVPIYQEVARRVGFERMQAYVDAFDYGNRQLGGVIDQFWLRGPLEISALEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYQPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALEVWPTL"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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-898", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43307", "model_name": "OXA-898", "model_type_id": "40292"}, "3820": {"model_id": "3820", "ARO_accession": "3005085", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "AAC(3)-IIg is part of the AAC(3) family. It was initially found in clinical isolates of Enterobacter cloacae.", "model_sequences": {"sequence": {"6120": {"dna_sequence": {"partial": "0", "sequence": "ATGAACACAAGGGAAACAATTGCGGCGGACCTTTCACGGCTGGGTGTCCAATCCGGCGCTCTCGTCATGGTTCACGCATCGCTGAAGGCGATCGGCCCCGTCGATGGAGGCGCAGCATCGATAGTGTCTGCCCTGCTCGATGCCGTCGGCCCCACTGGAAGCTTGATGGGATACGCCTCGTGGGACCGGTCGCCTTACGAAGAAACGCTCAATGGCGCACGGATGGATGCGGAACTGCGCCACCGATGGCCGCCGTTCGATCCAGCCATATCAGGCACGTATCGCGGCTTCGGCCTGCTCAACCGGTTCCTCCTCCAGACACCCGGCGCCCGGCGCAGCGCGCACCCGGATGCCTCGATGGTCGCGGTAGGGCCTCTGGCCGGCACTCTGACGCGGCCTCACGAACTTGGGCAGGCTTTCGGACCTGGATCGCCGCTGGAGCGTTTCGTCGAGCGTGCCGGAAAGGTTCTGTTGCTCGGAGCCCCGCTCGATTCCGTTACCGTCCTGCACTACGCCGAGGCCATTGCCCGCATCCCGAACAAGCGACGCGTGAGCTACGAAATGCCGATCCGCAGCGAGGACGGCGGAGTGAGATGGAAACGCGCCGAGGATTTCGACTCCAACGGCATTCTCGATTGTTTCGCTATCGAAGGAGAGCCGGACGCCGTCGAGACAATTACCAATGCCTATGTGGAGCTGCGACGCCATCGGGAGGGCTTGGTCGGTCAGGCGCACTGCTACTTGTTCGAAGCGCGGGATATCGTTTCGTTCGGTGTCGACTATCTTCAACGGCACTTTGGCTCGCCCTGA", "fmax": "810", "accession": "MT090547.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "QKT21444.1", "sequence": "MNTRETIAADLSRLGVQSGALVMVHASLKAIGPVDGGAASIVSALLDAVGPTGSLMGYASWDRSPYEETLNGARMDAELRHRWPPFDPAISGTYRGFGLLNRFLLQTPGARRSAHPDASMVAVGPLAGTLTRPHELGQAFGPGSPLERFVERAGKVLLLGAPLDSVTVLHYAEAIARIPNKRRVSYEMPIRSEDGGVRWKRAEDFDSNGILDCFAIEGEPDAVETITNAYVELRRHREGLVGQAHCYLFEARDIVSFGVDYLQRHFGSP"}}}}, "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."}, "36461": {"category_aro_name": "AAC(3)", "category_aro_cvterm_id": "36461", "category_aro_accession": "3000322", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Acetylation of the aminoglycoside antibiotic on the amino group at position 3."}, "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": "AAC(3)-IIg", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43296", "model_name": "AAC(3)-IIg", "model_type_id": "40292"}, "3791": {"model_id": "3791", "ARO_accession": "3005047", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "eptB is a phosphoethanolamine transferase. It confers resistance to peptide antibiotics.", "model_sequences": {"sequence": {"6086": {"dna_sequence": {"partial": "0", "sequence": "GTGCCACAGCGTCAGGCGGTGTTTTATTCTTCTTTTTCCAGGTTTGCTTGCATGAAATATATTAGAACGATGACGCAGCAGAAGCTTAGTTTTTGGCTGGCGCTGTACATCGGCTGGTTTATGAACGTCGCCGTTTTTTTCCGGCGTTTCGATGGTTATGCTCAAGAGTTCACTTTCTGGAAAGGGCTTTCCGGTGTTGTTGAACTGGTTGCCACGGTATTTGTCACCTTCTTCCTGTTACGTCTTCTGTCGCTGTTCGGCCGCCGTATCTGGCGCATTCTGGCGACGCTGATTGTCCTGTTTTCCGCCGCGGCGAGTTACTACATGACGTTCCTCAATGTGGTGATTGGCTACGGGATTATCGCTTCGGTGATGACCACCGATATCGACCTGTCGAAAGAGGTCATCGGCTGGCACCTGATCCTCTGGCTGGTGGTGGTGAGCGCGCCGCCGTTGCTGTTCATCTGGAGCAACCGCTGCCGCCATACGCTGCTGCGCCAGCTGCGCACCCCGGGCCAGCGGGTTAAAAACGTGCTGATCGTGGTGCTGGCCGGACTGATTGTCTGGGGACCCATCCGCCTGCTAGAGCTGCGCCAGCATGATGTGGAGCGCCATTCGGAAGTGGATATGCCGAGCTATGGCGGGGTGATCGCCAACTCTTACCTGCCGTCGAACTGGTTGTCGGCGCTGGGACTGTACGCCTGGGCGCAGGTGGATGAATCCTCAGACAACAAATCGCTGATTAACCCGGCGAAGAAGTTCACCTACGTCGCGCCGGAAGGTCTGGATGATACCTACGTGGTGTTTATCATTGGCGAAACGACCCGCTGGGACCATATGGGCATCCTCGACTATAGCCGCAATACCACGCCAGAGCTGGAGAAAGAGAAGAATCTCGTCGCCTTCCGCGGTTACTTGTGCGATACCGCTACCAAACTGTCGTTACGCTGCATGTTTGTGCGCGAGGGCGGGGCGGAAGATAACCCCCAGCGGACGCTCAAAGAGCAGAATGTCTTTGCCGTGCTGCATCAGCTGGGCTTCAGCGGCAATCTGTACGCCATGCAGAGCGAGATGTGGTTCTACAGCAACACGATGGCCAACAATATCGCCTACCGCGAGCAGATTGGCGCCGAGCCGCGCAACCGCGGTAAGAGCGTTGACGATATGCTGCTGGTGGATGAGATGAAGCGCGGTATGGCGCAGGGCAACGCCTCCGGTAAGCATCTGATCATTCTCCACACCAAAGGCTCCCACTTTAACTACACCCAACGCTACCCGCGCAGCTTCGCCCAGTGGAAACCGGAGTGCGTCGGCGTCGACAACAAGTGCTCGAAAGCGGAACTGATCAATTCCTACGACAATAGCGTGACCTATGTCGATCACTTTATCGTCAGCGTCCTCGACCAGCTGCGGGATAAGAAAGCGATTGTGTTCTATGCCGCCGACCACGGGGAGTCGATTAACGAGCGTGAACACCTGCACGGTACGCCGCGCAAGATGGCGCCGCCGGAGCAGTTCCGCGTGCCGATGATGGTGTGGATGTCGGATAAGTACCTGGAAAATCCCGATCACGCCGCCGCGTTTGCCCATCTGCAGCAGCAGGCTGCGATGAAGGTGCCGCGCCGTCACGTCGAGCTGTACGACACCATTATGGGCTGCCTCGGCTATACCTCGCCGGATGGCGGGATCAATGAGAACAACAACTGGTGCCGGTGGAAAAAGTAA", "fmax": "5125365", "accession": "FO203501.1", "fmin": "5123640", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae subsp. rhinoscleromatis SB3432", "NCBI_taxonomy_id": "861365", "NCBI_taxonomy_cvterm_id": "43247"}, "protein_sequence": {"accession": "CCI79240.1", "sequence": "MPQRQAVFYSSFSRFACMKYIRTMTQQKLSFWLALYIGWFMNVAVFFRRFDGYAQEFTFWKGLSGVVELVATVFVTFFLLRLLSLFGRRIWRILATLIVLFSAAASYYMTFLNVVIGYGIIASVMTTDIDLSKEVIGWHLILWLVVVSAPPLLFIWSNRCRHTLLRQLRTPGQRVKNVLIVVLAGLIVWGPIRLLELRQHDVERHSEVDMPSYGGVIANSYLPSNWLSALGLYAWAQVDESSDNKSLINPAKKFTYVAPEGLDDTYVVFIIGETTRWDHMGILDYSRNTTPELEKEKNLVAFRGYLCDTATKLSLRCMFVREGGAEDNPQRTLKEQNVFAVLHQLGFSGNLYAMQSEMWFYSNTMANNIAYREQIGAEPRNRGKSVDDMLLVDEMKRGMAQGNASGKHLIILHTKGSHFNYTQRYPRSFAQWKPECVGVDNKCSKAELINSYDNSVTYVDHFIVSVLDQLRDKKAIVFYAADHGESINEREHLHGTPRKMAPPEQFRVPMMVWMSDKYLENPDHAAAFAHLQQQAAMKVPRRHVELYDTIMGCLGYTSPDGGINENNNWCRWKK"}}}}, "ARO_category": {"41433": {"category_aro_name": "pmr phosphoethanolamine transferase", "category_aro_cvterm_id": "41433", "category_aro_accession": "3004269", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane."}, "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."}, "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."}}, "ARO_name": "eptB", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43246", "model_name": "eptB", "model_type_id": "40292"}, "3790": {"model_id": "3790", "ARO_accession": "3005046", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "This MecI is a methicillin-resistant repressor resembling MecC. It confers resistance to penams.", "model_sequences": {"sequence": {"6085": {"dna_sequence": {"partial": "0", "sequence": "ATGACACGTGAAGGCTATGATATATCAGCGTCAGAATGGGAAATAATGAATACGATTTGGAATAAAAAATTAATAAGTGCTAATGACGTTATAGAAATAGTACAAAAGCACAAGGAATGGAGTCCAAAAACAATAAGAACACTAATCAATCGTCTTTACAAAAAGAAATTCATAGATAGAACAAGTCGAAATAAAATTTTTGAATATTTCCCAATAGTAGAGGAAAAAGATATGAAGTACAAAACGTCTAAAGTGTTTTTGGATAAAGTGTATGAAGGTGGATTAAATTCATTAGTCTTAAATTTTGTTGAAAATGAAGAATTGTCCGAAGATGATATTGAAGAATTGAAAAATATATTAAATAATAAATATTAA", "fmax": "39904", "accession": "FR821779.1", "fmin": "39529", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus aureus subsp. aureus LGA251", "NCBI_taxonomy_id": "985006", "NCBI_taxonomy_cvterm_id": "42590"}, "protein_sequence": {"accession": "CCC86797.1", "sequence": "MTREGYDISASEWEIMNTIWNKKLISANDVIEIVQKHKEWSPKTIRTLINRLYKKKFIDRTSRNKIFEYFPIVEEKDMKYKTSKVFLDKVYEGGLNSLVLNFVENEELSEDDIEELKNILNNKY"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "37589": {"category_aro_name": "methicillin resistant PBP2", "category_aro_cvterm_id": "37589", "category_aro_accession": "3001208", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams."}, "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": "MecC-type methicillin resistance repressor MecI", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43245", "model_name": "MecC-type methicillin resistance repressor MecI", "model_type_id": "40292"}, "3793": {"model_id": "3793", "ARO_accession": "3005051", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LpsB is involved in lipopolysaccharide synthesis. It confers intrinsic resistance to colistin and other peptide antibiotics.", "model_sequences": {"sequence": {"6088": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAGTGATGCAACTTCTCCCAGAACTCAATAGCGGTGGCGTAGAACGCGGCACACTGGAAATTGCACGTGCACTGGTTGCACAAGGTCATCAGTCTCTAGTTGTGTCTAATGGCGGGCGTTTGGTCTCACAACTTGAAGCTGAAGGTTCCACACACTTAACACTGCCGATTCATAAAAAATCATTGTCGAGCTTGTGGCAAATCCGTCCATTACGTCAGCTTATTGAAGAACACCAACCAGACATTGTACATGTGCGCTCTCGCGTACCTGCATGGCTAACCCACTTCGCTTTAAGAAAAATACCAGCGAATAAACGCCCTCACCTCATTAGCACGGTACATGGTTTCTATTCAGTTAATCGTTATAGTGCGATCATGACTCAGGCAGAAAAAGTGATCGCTGTTTCTGACAGCGTAGTTAAATACATCACAGGCCATTATAAAAACTGTCCACCACAAGATATTATCCGGATTTATCGAGGAATTGACCCTGCCGCTTTTCCGCATAACTATCAACCTTCAGCACAGTGGTTTAACCAAGTCTTTAACGACTTTCCCGAACTTGAAAATAAATTTTTACTTTGCCTACCTGGCCGTATTACTCGTTTAAAAGGACATGAAAGTTTAATTGAACTGATGCAGCAACTTCATTCGCAATATCCTCAACTGCATGCTGTTGTTGTAGGTGGGGCTGATGTAAAAAAACAAGCCTATTTAAGTGAGTTGCAAAACACCATTCAAAGCAAAGGACTTGCAGATAAAATTACATTTGTAGGACATCGCTCAGATATACGCGAATGGCTCGCTTTTAGCGATATAGTGCTCTCTCTATCCAATCAAGCAGAAACATTCGGTAGAACAGCATTAGAAGCGCTCTCTGTCGGTACGCCGGTCATTGGCTGGAACCGTGGAGGTGTTGCCGAGATTTTATCTCATGTGTACCCGCAGGGTCTTGTTGAAGCAGAAAATGAAAAAGCTTTATTAGAAATAGTAAAGCATCATATTGAACAACCTCAAACAGTCGCTCCTGTGACAATGTTTAGTTTAAAAGATATGTGTGACCAAACCCTTGAGCTATATCAAAGTGTATTGAAATAA", "fmax": "522372", "accession": "CP045110.1", "fmin": "521271", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "QFQ03949.1", "sequence": "MKVMQLLPELNSGGVERGTLEIARALVAQGHQSLVVSNGGRLVSQLEAEGSTHLTLPIHKKSLSSLWQIRPLRQLIEEHQPDIVHVRSRVPAWLTHFALRKIPANKRPHLISTVHGFYSVNRYSAIMTQAEKVIAVSDSVVKYITGHYKNCPPQDIIRIYRGIDPAAFPHNYQPSAQWFNQVFNDFPELENKFLLCLPGRITRLKGHESLIELMQQLHSQYPQLHAVVVGGADVKKQAYLSELQNTIQSKGLADKITFVGHRSDIREWLAFSDIVLSLSNQAETFGRTALEALSVGTPVIGWNRGGVAEILSHVYPQGLVEAENEKALLEIVKHHIEQPQTVAPVTMFSLKDMCDQTLELYQSVLK"}}}}, "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."}, "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."}, "43251": {"category_aro_name": "Intrinsic peptide antibiotic resistant Lps", "category_aro_cvterm_id": "43251", "category_aro_accession": "3005050", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "lpsB is involved in lipopolysaccharide synthesis. It provides intrinsic resistance to colistin and other peptide antibiotics such as polymyxins."}}, "ARO_name": "LpsB", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43252", "model_name": "LpsB", "model_type_id": "40292"}, "3792": {"model_id": "3792", "ARO_accession": "3005049", "model_param": {"blastp_bit_score": {"param_value": "250", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CrcB is part of the Camphor Resistance Protein Family. It confers resistance to aminoglycoside antibiotics.", "model_sequences": {"sequence": {"6087": {"dna_sequence": {"partial": "0", "sequence": "GTGCTTAATTTTACTATTCTGATCTTTGTTGGCGGGGCGTTTGGCGCAATATGCCGCGAATTATTGATGTTGGTAGTGCCTCGCCTGAGCGATGGCTTTCCCCTGGATATCTTCATCGCCAATATTATTGCCGCTTTTTTGCTTGGTTTATGCACATCACTGTATAAAAGGAACCGGGTTAATCAGTACATCCATATGATGGTGGCTACGGGTATCATGGGAGGGCTATCAACCTTCTCCAGCTTTGTATCTGGCGCGGTGGAAATGATGAATGAGCCACTCAGCGCGCTGATCGCCATCTGTTATCTGGTTATCAGCCTGATAGTCGGTTTTATGGCTGTGGAGCTGGGGTTAAGACTGGGCTCCCGAGTAAAGCCTGCGCCGCCCATGACTCATAACAGATCGACTGGTTAA", "fmax": "4177223", "accession": "HF536482.1", "fmin": "4176809", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae subsp. pneumoniae Ecl8", "NCBI_taxonomy_id": "1226680", "NCBI_taxonomy_cvterm_id": "43250"}, "protein_sequence": {"accession": "CCN31428.1", "sequence": "MLNFTILIFVGGAFGAICRELLMLVVPRLSDGFPLDIFIANIIAAFLLGLCTSLYKRNRVNQYIHMMVATGIMGGLSTFSSFVSGAVEMMNEPLSALIAICYLVISLIVGFMAVELGLRLGSRVKPAPPMTHNRSTG"}}}}, "ARO_category": {"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."}, "36251": {"category_aro_name": "multidrug and toxic compound extrusion (MATE) transporter", "category_aro_cvterm_id": "36251", "category_aro_accession": "3000112", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates."}, "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": "CrcB", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43249", "model_name": "CrcB", "model_type_id": "40292"}, "3805": {"model_id": "3805", "ARO_accession": "3005067", "model_param": {"blastp_bit_score": {"param_value": "800", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ParS is the sensor component of the two-component ParRS system. Alongside its counterpart ParR, it confers resistance to polycationic antibiotics though regulation of efflux pumps and porins.", "model_sequences": {"sequence": {"6100": {"dna_sequence": {"partial": "0", "sequence": "ATGCTGCGCCTGTTCCTGCGCCTCTACCTGCTGCTGGCCCTGGGGTTCGCCGCCGCGATCTTCGTGGTCGACCATGTCATCGACGCGTTCTACGACAGCATCGTCGAGAACTATCACCGCGACGCCGTTCGCGGCCAGGCCTATTCGCTGGTGGAAAAGCTGGCCCCGCTGGACCAGGCCGGACGCCAGCGACAGCTCGAAGACTGGCGTCCCCACTACGGGCTCGAGCTGAGCCTGACGGATGCCAGGCAGGCGAAGCTGACGCAGGAAGAGCAGGCCCTCCTCGACAAGAACCTGCTGGTGGTACGCGAGGACTTCACGGAATTCATCAGCCGCATCGACGCGGGCCCGCAACTGCTCGACATCAAGCTGCCGCCGGAACCCTCGCTGACCCCACTATTCACCGTGCTGGCCTACATCCTGCTCGGCGTGCTGGTCGGCATCGCCCTGCTGGTATGGGTCCGCCCGCACTGGCGCGACCTCGAGACCCTGCGCCTGGCCGCGCAACGCTTCGGCGACGGCGACCTGTCATCGCGCACGCGCATTTTCCGACGCTCCGACATCCGCACCCTGGCCCAGCACTTCAACCAGATGGCCGACCGCATCGAAAGCCTGATCAGCAACCAGCGTGAACTGACCAACGCGGTATCCCACGAATTGCGCACGCCGATCTCCCGCCTGTCCTTCGAACTCGAGCAATTGAACAAGCAGGTCGACGCCGAAGTACGCCACGACCTGATAGAGGACATGCGCGCCGATCTCGGCGAACTGGAGGAAATGGTCTCCGAACTGCTGACCTACGCCCGCCTGGAGCACGGCAACGTCGGGAGCCACCGGGAAATCGTCGACGCCGCGAGCTGGCTGGATAGCGTCGTCGCCGACGTCGCCCTGGAAGCCGAAGCCGCCGGAGTCACCTGCGAGATCAGCGCCTGCCAGGTCGAACAGATCCGCATCGAGCCTCGCTTCATGGCGCGCGCAGTGATCAACCTGCTGCGCAACGCCATTCGCCACGCACACTCGCGCGTCGAAATCGCCCTCCTCGATCAAGGCGACAGCTGTCAGATACGGGTCAACGACGACGGCCCCGGGATACCGGCGGACGCCCGGCAGAAGATCTTCGAACCCTTTTCGCGCCTGGACGACAGCCGCGATCGCAGCACCGGCGGCTTCGGCCTGGGCCTGGCGATCGTCCACCGGGTCGCGCAATGGCACGGCGGCTATGCGGAAGCGCTGGAAACGCCGCAGGGAGGCGCCTCCTTCCGCCTGACCTGGGAGCGACCCCGTTGA", "fmax": "1951725", "accession": "AE004091.2", "fmin": "1950438", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "AAG05187.1", "sequence": "MLRLFLRLYLLLALGFAAAIFVVDHVIDAFYDSIVENYHRDAVRGQAYSLVEKLAPLDQAGRQRQLEDWRPHYGLELSLTDARQAKLTQEEQALLDKNLLVVREDFTEFISRIDAGPQLLDIKLPPEPSLTPLFTVLAYILLGVLVGIALLVWVRPHWRDLETLRLAAQRFGDGDLSSRTRIFRRSDIRTLAQHFNQMADRIESLISNQRELTNAVSHELRTPISRLSFELEQLNKQVDAEVRHDLIEDMRADLGELEEMVSELLTYARLEHGNVGSHREIVDAASWLDSVVADVALEAEAAGVTCEISACQVEQIRIEPRFMARAVINLLRNAIRHAHSRVEIALLDQGDSCQIRVNDDGPGIPADARQKIFEPFSRLDDSRDRSTGGFGLGLAIVHRVAQWHGGYAEALETPQGGASFRLTWERPR"}}}}, "ARO_category": {"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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "35933": {"category_aro_name": "gentamicin C", "category_aro_cvterm_id": "35933", "category_aro_accession": "0000014", "category_aro_class_name": "Antibiotic", "category_aro_description": "Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}, "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."}, "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."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "36193": {"category_aro_name": "acridine dye", "category_aro_cvterm_id": "36193", "category_aro_accession": "3000054", "category_aro_class_name": "Drug Class", "category_aro_description": "Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents."}, "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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."}, "35963": {"category_aro_name": "acriflavine", "category_aro_cvterm_id": "35963", "category_aro_accession": "0000045", "category_aro_class_name": "Antibiotic", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}, "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."}, "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."}, "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."}, "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": "ParS", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43271", "model_name": "ParS", "model_type_id": "40292"}, "3801": {"model_id": "3801", "ARO_accession": "3005061", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "A novel aminoglycoside resistance gene identified from Cupriavidus gilardii; AAC(3)-IVb / aacC10 is an aminoglycoside-3-N-acetyltransferase gene which confers resistance to gentamicin and tobramycin", "model_sequences": {"sequence": {"6130": {"dna_sequence": {"partial": "0", "sequence": "TTGGTGACCCAGTTGCGCGCGCTCGGCGTGCCACCCGGCGCCGTGCTGCTGGTCCACGCGTCGTTCCGCTCGATCAGGCCCGTGCAAGGGGGCCCACAAGGATTGATCGAGGCGCTGCGGGAAGCGGCCGGCCCTGCCGGCACGCTGGTGATGCCGTCGTGGGGCGATGACGATGACGCGCCCTTCGACCCGGCCGCCACGCCGGCAGCGGCGGACCTTGGCGCGGTCGCCGATGCCTTCTGGCGACTGCCCGACGTGGTTCGCAGCCACCACCCGTTTGCCTTCGCGGCGGCGGGACCGCAGGCGCATCGAATCACCGCGGATCCCTTGCCGTTGCCGCCCCATATTCCGGCCAGCCCGGTCGGCCGCGTGCACGAGCTCGATGGACAGGTGCTGCTGCTTGGCGTGGGCCATGACGCCAACACCACGATCCATCTGGCCGAACTGATGGCCGGCGTGCCTTACGGCGTGCCGCATCACTGCACGGTGCTGCGGGACGGCAAGCCGGCTCGCATCGACTATCTCGAAAACGACCACTGCTGCCAGCGCTTCGATCTGGTGGACGGATGGCTCAAGGAAAAGGGCCTTCAGCGTGAAGGCCCAGTTGGCAATGCCGGCGCCCGCTTGATGCGGGCGCGGGACATCGTCGATGTCGTGCGGCAGCAGTTGGCTCGCGATCCGCTCGTCTTCCTGCATCCGCCTCAGGTTGGCTGCGAGGAGTGCGATGCCGCGCGGCGGTCGGTCAGCACCAAGTAG", "fmax": "756", "accession": "MN366378.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Cupriavidus gilardii", "NCBI_taxonomy_id": "82541", "NCBI_taxonomy_cvterm_id": "43264"}, "protein_sequence": {"accession": "QEQ43476.1", "sequence": "MVTQLRALGVPPGAVLLVHASFRSIRPVQGGPQGLIEALREAAGPAGTLVMPSWGDDDDAPFDPAATPAAADLGAVADAFWRLPDVVRSHHPFAFAAAGPQAHRITADPLPLPPHIPASPVGRVHELDGQVLLLGVGHDANTTIHLAELMAGVPYGVPHHCTVLRDGKPARIDYLENDHCCQRFDLVDGWLKEKGLQREGPVGNAGARLMRARDIVDVVRQQLARDPLVFLHPPQVGCEECDAARRSVSTK"}}}}, "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."}, "36461": {"category_aro_name": "AAC(3)", "category_aro_cvterm_id": "36461", "category_aro_accession": "3000322", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Acetylation of the aminoglycoside antibiotic on the amino group at position 3."}, "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."}, "40942": {"category_aro_name": "gentamicin A", "category_aro_cvterm_id": "40942", "category_aro_accession": "3004015", "category_aro_class_name": "Antibiotic", "category_aro_description": "Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death."}, "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."}}, "ARO_name": "AAC(3)-IVb", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43265", "model_name": "AAC(3)-IVb", "model_type_id": "40292"}, "3759": {"model_id": "3759", "ARO_accession": "3002653", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "APH(3')-VIb is a plasmid-encoded aminoglycoside phosphotransferase in K. pneumoniae and S. marcescens", "model_sequences": {"sequence": {"6049": {"dna_sequence": {"partial": "0", "sequence": "ATGGAATTGCCCAATATTATTCAACAATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGTGAAGCGAAAATGTTGAGTTGGCTCTCTGATAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTCATGATCACTAAAGCGATCAATGCAAAATCAATTTCAGCGCTTTTTTTAACAGAGCAAGAATTGCTTGCTATCTATAAGGAAACACTCAATCAGTTAAATGCAGTTGCTATTATTGATTGCCCATTTATTTCAAGCATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGAGATAGATCAAGATGATTTTGAGGCTGAATTATGGGGAGACCATAAAACTTACATAAGTCTTTGGAATGAGTTAAATGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATCTGGTGAAATTTACTTTTTAGATCTTGGTCGTGCTGGATTAGCAGATGAATTTGTAGATATATCTTTTGTTGAACGTTGCCTAAGAGAGGATGTATCTGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAAAACGATATGCCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA", "fmax": "5713", "accession": "AJ627643.4", "fmin": "4933", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Alcaligenes faecalis", "NCBI_taxonomy_id": "511", "NCBI_taxonomy_cvterm_id": "43206"}, "protein_sequence": {"accession": "CAF29483.1", "sequence": "MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSDKLKVPELIMTFQDEQFEFMITKAINAKSISALFLTEQELLAIYKETLNQLNAVAIIDCPFISSIDHRLKESKFFIDNQLLDEIDQDDFEAELWGDHKTYISLWNELNETRVEERLVFSHGDITDSNIFIDKSGEIYFLDLGRAGLADEFVDISFVERCLREDVSEETAKIFLKHLKNDMPDKRNYFLKLDELN"}}}}, "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."}, "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."}, "35940": {"category_aro_name": "ribostamycin", "category_aro_cvterm_id": "35940", "category_aro_accession": "0000021", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}, "37001": {"category_aro_name": "paromomycin", "category_aro_cvterm_id": "37001", "category_aro_accession": "3000657", "category_aro_class_name": "Antibiotic", "category_aro_description": "An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes."}, "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."}, "36265": {"category_aro_name": "APH(3')", "category_aro_cvterm_id": "36265", "category_aro_accession": "3000126", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'"}, "36999": {"category_aro_name": "gentamicin B", "category_aro_cvterm_id": "36999", "category_aro_accession": "3000655", "category_aro_class_name": "Antibiotic", "category_aro_description": "Gentamicin B is a semisynthetic aminoglycoside antibacterial."}, "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."}, "36996": {"category_aro_name": "isepamicin", "category_aro_cvterm_id": "36996", "category_aro_accession": "3000652", "category_aro_class_name": "Antibiotic", "category_aro_description": "A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae."}, "36997": {"category_aro_name": "G418", "category_aro_cvterm_id": "36997", "category_aro_accession": "3000653", "category_aro_class_name": "Antibiotic", "category_aro_description": "A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3')."}, "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."}, "35943": {"category_aro_name": "butirosin", "category_aro_cvterm_id": "35943", "category_aro_accession": "0000024", "category_aro_class_name": "Antibiotic", "category_aro_description": "Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}}, "ARO_name": "APH(3')-VIb", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39053", "model_name": "APH(3')-VIb", "model_type_id": "40292"}, "3753": {"model_id": "3753", "ARO_accession": "3005008", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "TxR is a putative transcription regulator that plays a role in conferring tetracycline resistance. It is required for proper functioning of Tet35.", "model_sequences": {"sequence": {"6043": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAGTGCAAAAATGCAAAGCTACGATACACAGACGTTCTTTGGATGCAGACCCATTACTTCCTCTTATTGGTAATAGCACTTGCATCAGTGAACTACGTAACAAACTCAAAAAATACGCGCAATGTGATGCGGAAGTACTCATCCAAGGCGAAACCGGGGTGGGCAAAGGTATGTGTGCTCGAATCATTCACGAACTTTCAAGTAGACATATATACCCATTTGTTGAAGTTAACTGCGGAGCGATTCCAAGCGGACTCATCGCATCAGAGCTCTTCGGTCATGAGAAAGGAGCATTTACGGGGGCGATTTCGGATCGAATCGGCTTCATTCAAAAAGCGAACAAAGGGACGCTATTTCTCGATGAAATCGGCGACATGCCGCCTGATCTACAAATTCATTTGCTGCATTTTTTGGAGAGTAAGCAAATCCATAAAGTTGGTGCAGACAAAATCATTGATGTGGATTGCCGCGTCATCGCAGCCAGCCATGTAGATTTAAAAAGTGAAGTAATACAAGGAGGATTCCGAGAGGATTTATTTTACCGACAAAACATACTACCACTCACTATCCCCCCACTTCGAAAGCGTGGTGAGGATACGGTCATATTGTCAGAGCGTTTTTTAGAAGAATTATCCAACGGAAAAGTTCAGAGTATGTCTCCGGAAGTGAAGAAAAAGCTACTGAAACATAAATGGCCCGGCAACGTGAGAGAGCTGCGCAATGTCATTCAAAGGGCGATTGTAATGTGTGAGGATAACACTCTTCACATCGCCGATCTCGGCTTGGACAATAACGAAAGACAGCTCCTTCCCTCTGTTGAACAAATTGACTTAGATTATTTGTTAAAAGCAATCGAAGACAACAAACACAACATGAGTGCGGCTGCGAGGAATTTAGGTATTTCTAGAACCACACTCTACCGTCTAATCAAGAAATATAACCTGCCCATCTAA", "fmax": "1920", "accession": "AF353562.1", "fmin": "963", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio harveyi", "NCBI_taxonomy_id": "669", "NCBI_taxonomy_cvterm_id": "36785"}, "protein_sequence": {"accession": "AAK37618.1", "sequence": "MKVQKCKATIHRRSLDADPLLPLIGNSTCISELRNKLKKYAQCDAEVLIQGETGVGKGMCARIIHELSSRHIYPFVEVNCGAIPSGLIASELFGHEKGAFTGAISDRIGFIQKANKGTLFLDEIGDMPPDLQIHLLHFLESKQIHKVGADKIIDVDCRVIAASHVDLKSEVIQGGFREDLFYRQNILPLTIPPLRKRGEDTVILSERFLEELSNGKVQSMSPEVKKKLLKHKWPGNVRELRNVIQRAIVMCEDNTLHIADLGLDNNERQLLPSVEQIDLDYLLKAIEDNKHNMSAAARNLGISRTTLYRLIKKYNLPI"}}}}, "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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "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."}, "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."}}, "ARO_name": "TxR", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43196", "model_name": "Txr", "model_type_id": "40292"}, "3797": {"model_id": "3797", "ARO_accession": "3005056", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Tet(X6) is a tetracycline inactivating enzyme. It is a Tet(X) variant.", "model_sequences": {"sequence": {"6092": {"dna_sequence": {"partial": "0", "sequence": "ATGACTTTACTAAAACATAAAAAAATTACAATAATTGGTGCCGGGCCTGTTGGATTAACAATGGCGAGATTGTTACAGCAAAACGGCGTGGACATTACAGTTTACGAGAGAGACAAAGACCAAGATGCAAGGATTTTTGGTGGGACACTTGATCTGCACAGGGATTCGGGACAGGAAGCAATGAAAAGAGCGGGATTGTTACAAACTTATTATGACTTAGCTTTACCAATGGGTGTAAATATTGTTGATGAAAAGGGCAATATTTTAACCACAAAAAATGTAAGACCCGAAAATCGTTTTGACAATCCTGAAATAAACAGAAATGACTTAAGGACTATCCTATTAAATAGTTTACAAAATGATACCGTCATTTGGGATAGAAAACTTGTTACCCTTGAACCTGATAAGGAGAAGTGGATACTAACTTTTGAGGATAAATCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCGGAGGTGAACTGTCCTGGATTTTTTCAGCTTTGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAGCAAAACGCGGGTAGATTTTCAAGACAGAAATAGTGTCGTTGATTTTCTCCTGAAAAAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTTTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGATAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGTGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTGCTTATGGAAGAGAAGCACAGGCAGAATCAATAATAAACGAAACGGAAATGTTCAGCCTCGACTTTTCTTTCCAAAAACTAATGAATCTATAA", "fmax": "37258", "accession": "MN507533.1", "fmin": "36121", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Proteus genomosp. 6", "NCBI_taxonomy_id": "1311820", "NCBI_taxonomy_cvterm_id": "43258"}, "protein_sequence": {"accession": "QIM09823.1", "sequence": "MTLLKHKKITIIGAGPVGLTMARLLQQNGVDITVYERDKDQDARIFGGTLDLHRDSGQEAMKRAGLLQTYYDLALPMGVNIVDEKGNILTTKNVRPENRFDNPEINRNDLRTILLNSLQNDTVIWDRKLVTLEPDKEKWILTFEDKSSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKSKTRVDFQDRNSVVDFLLKKFSDWDERYKELIRLTSSFVGLATRIFPLDKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFAYGREAQAESIINETEMFSLDFSFQKLMNL"}}}}, "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."}, "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."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}, "ARO_name": "Tet(X6)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43257", "model_name": "Tet(X6)", "model_type_id": "40292"}, "3812": {"model_id": "3812", "ARO_accession": "3005076", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-6 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.", "model_sequences": {"sequence": {"6107": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTTTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTCGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "1307", "accession": "KJ910989.1", "fmin": "389", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AIW80558.1", "sequence": "MLNKLKIGTLLLLTLTACLPNFVHSVTSNPQPASAPVQQSATQATFQQTSANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43283", "model_name": "ROB-6", "model_type_id": "40292"}, "3761": {"model_id": "3761", "ARO_accession": "3005018", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LMB-1 is a subclass B3 metallo-beta-lactamase that confers resistance to penams, cephalosporins, and carbapenems.", "model_sequences": {"sequence": {"6051": {"dna_sequence": {"partial": "0", "sequence": "ATGACGTTAGCTAAAAGTTTTCGCTGTTTTTGCCTTGTAACTACATTAAGTTCGATGGCTATGCTGGCCGGTTGCGGCGGCACAGCCCCGGTAACAGTATTAAGCCCACCGCCAGCAGACTGGGTTAACAGCTGTAAAGACTGGGATGACTGGGACAAAGCCGGGCCGCCGTATCGGATTTATGGCAACAGTTACTATGTGGGCACCTGTGGTATCAGCGCTATTTTGATCACCGGTGATAACGGCCATATTCTGATCGATGGCGCCACTGAAGCGGGTGCAAAGGTAATTGCTGCCAATATCGACAGGCTGGGTTTTTCACTGCGTGATGTAAAGTTGCTACTGCAAAGCCATGAGCATTTCGATCATGTGGCCGGTTTGGCGCAGTTACAGCAACAAAGCGGCGCCAAACTGCTGGCATCGCCTGCAGCAGCACCGGTGTTAACCAGTGGCGTGGTAGCCGCTGCCGATCCGCAAGCGGGCATGCACGAGCCGTTTCCAGCCGTTAGGGTAGATGGCCTGGTTACAGCAGGCCAGGTGGTTACCCTGGGCAAGCTAAGCCTGCTGCCTGTGGCAACGCCGGGGCATACCCCTGGCGCCTTAAGCTGGCAGTGGAGCAGTTGCGAAGCCGGGCAGTGTCAGGTACTGGTGTACGCCGACAGCTTATCGCCGGTTAGCAGCGACAGTTATCGTTTTAGCGAGCACCTTACTTATCTCAATGCATACCGGGCCAGTTTGCATAAACTGGCAGCGCTTGATTGCCAGATCCTGCTTACGCCCCATCCGTCAGCCAGTAATATGCGTACGCGGCTGCAAAGCAGTGCAGGTTTAACAGATACCCAAGGCTGCGTAGTTTATGCAGACGCGATAACACAGCGGCTCGAGCAGCGTTTAATAAAGGAAACAACGCAGTAA", "fmax": "159263", "accession": "MH475146.1", "fmin": "158348", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter freundii", "NCBI_taxonomy_id": "546", "NCBI_taxonomy_cvterm_id": "36915"}, "protein_sequence": {"accession": "AYD68552.1", "sequence": "MTLAKSFRCFCLVTTLSSMAMLAGCGGTAPVTVLSPPPADWVNSCKDWDDWDKAGPPYRIYGNSYYVGTCGISAILITGDNGHILIDGATEAGAKVIAANIDRLGFSLRDVKLLLQSHEHFDHVAGLAQLQQQSGAKLLASPAAAPVLTSGVVAAADPQAGMHEPFPAVRVDGLVTAGQVVTLGKLSLLPVATPGHTPGALSWQWSSCEAGQCQVLVYADSLSPVSSDSYRFSEHLTYLNAYRASLHKLAALDCQILLTPHPSASNMRTRLQSSAGLTDTQGCVVYADAITQRLEQRLIKETTQ"}}}}, "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "43208": {"category_aro_name": "LMB beta-lactamase", "category_aro_cvterm_id": "43208", "category_aro_accession": "3005017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LMB is an AMR Gene family belonging to subclass B3 metallo-beta-lactamases."}, "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."}}, "ARO_name": "LMB-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43209", "model_name": "LMB-1", "model_type_id": "40292"}, "3762": {"model_id": "3762", "ARO_accession": "3005019", "model_param": {"blastp_bit_score": {"param_value": "496", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "IMP-68 is a subclass B1 metallo-beta-lactamase that confers resistance to carbapenems.", "model_sequences": {"sequence": {"6052": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAGGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA", "fmax": "738", "accession": "MF669572.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "ASU31903.1", "sequence": "MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPGHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}}, "ARO_name": "IMP-68", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43210", "model_name": "IMP-68", "model_type_id": "40292"}, "3806": {"model_id": "3806", "ARO_accession": "3005068", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ParR is a component of the two-component sensor ParRS. Alongside its counterpart ParS, it confers resistance to polycationic antibiotics through the regulation of efflux components and porins.", "model_sequences": {"sequence": {"6101": {"dna_sequence": {"partial": "0", "sequence": "ATGGACTGCCCTACCCTCAGCAAGGTATTGCTCGTCGAAGACGACCAGAAGCTCGCCCGCCTGATCGCCAGTTTCCTTTCCCAGCATGGTTTCGAAGTGCGCCAGGTGCATCGCGGTGATGCCGCGTTCGCCGCCTTCCTCGACTTCAAGCCGCAAGTGGTGGTTCTCGACCTCATGCTCCCCGGACAGAATGGTCTGCAGGTGTGCCGGGAGATCCGCCGGGTCGCGAACCTGCCGATCCTCATACTCACCGCCCAGGAGGACGATCTCGATCACATCCTCGGCCTGGAGTCCGGCGCCGACGACTACGTGATCAAGCCGATCGAGCCACCGGTGCTGCTCGCCCGCCTGCGCGCCCTGATGCGCCGGCACGCGCCCCTTCCCGCGTCCCCGGAAAGCCTGACATTCGGCAAGCTGAACATCGACCGACGGCGGCGCGAAGCGGAACTCGAAGGCCTCGGCATCGAACTGACCACGATGGAGTTCGAGCTGCTCTGGCTGCTGGCCAGCCAGGCAGGGGAAATACTTTCCCGCGACGAGATCCTCAACCAGATCCGCGGCATCGGTTTCGACGGCCTGAACCGCAGCGTCGACGTCTGCATCAGCAAGCTGCGCAATAAACTGAAGGACAATCCGCGCGAGCCGGTCCGGATCAAGACTGTCTGGGGCAAGGGCTACCTGTTCAACCCGCTGGGCTGGGAGCTCTGA", "fmax": "1952433", "accession": "AE004091.2", "fmin": "1951725", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "AAG05188.1", "sequence": "MDCPTLSKVLLVEDDQKLARLIASFLSQHGFEVRQVHRGDAAFAAFLDFKPQVVVLDLMLPGQNGLQVCREIRRVANLPILILTAQEDDLDHILGLESGADDYVIKPIEPPVLLARLRALMRRHAPLPASPESLTFGKLNIDRRRREAELEGLGIELTTMEFELLWLLASQAGEILSRDEILNQIRGIGFDGLNRSVDVCISKLRNKLKDNPREPVRIKTVWGKGYLFNPLGWEL"}}}}, "ARO_category": {"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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}, "35933": {"category_aro_name": "gentamicin C", "category_aro_cvterm_id": "35933", "category_aro_accession": "0000014", "category_aro_class_name": "Antibiotic", "category_aro_description": "Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}, "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."}, "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."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "36193": {"category_aro_name": "acridine dye", "category_aro_cvterm_id": "36193", "category_aro_accession": "3000054", "category_aro_class_name": "Drug Class", "category_aro_description": "Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents."}, "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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."}, "35963": {"category_aro_name": "acriflavine", "category_aro_cvterm_id": "35963", "category_aro_accession": "0000045", "category_aro_class_name": "Antibiotic", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}, "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."}, "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."}, "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."}, "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": "ParR", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43272", "model_name": "ParR", "model_type_id": "40292"}, "3816": {"model_id": "3816", "ARO_accession": "3005080", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-10 is a class A beta-lactamase from the blaROB AMR gene family. It was found in Glaesserella parasuis.", "model_sequences": {"sequence": {"6112": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAACCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "12175", "accession": "WIGU01000059.1", "fmin": "11257", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Glaesserella parasuis", "NCBI_taxonomy_id": "738", "NCBI_taxonomy_cvterm_id": "43288"}, "protein_sequence": {"accession": "MWQ02887.1", "sequence": "MFNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-10", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43287", "model_name": "ROB-10", "model_type_id": "40292"}, "3765": {"model_id": "3765", "ARO_accession": "3005024", "model_param": {"blastp_bit_score": {"param_value": "270", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FosL1 is related to FosA-like genes. It is a plasmid-encoded fosfomycin resistant gene found in E. coli.", "model_sequences": {"sequence": {"6055": {"dna_sequence": {"partial": "0", "sequence": "ATGCTTTCTGGTATGAATCACCTAACGCTCGCGGTTCAGTCTTTGGAACGTAGCGTTTCTTTTTATAAAGACACCCTTGGCTTTCGTTTGGCAGCAAGATGGAAAAATGGCGCCTACCTTGAGCTCGGAGATTTATGGTTGTGTCTATCACTTGACGATAAAAGGTCTGCGCAGCCTTGGCCTGAATACACGCACTACGCTTTTTCTGCCTTGGAACAAGATTTCTCCTCCTTTGTTGCCAAGCTAATTCAAAAAGGCGTCGTTGAATGGAAGAAAAACAGAAGCGAAGGAAATTCTTTTTACTTTCTTGACCCTGATGGACATAAGCTAGAGGTTCACGTAGGTAATTTAGAGTCTCGCTTGAAGCAATGTCGTGTGCATCCATATACAGATATGGAAATATTTGACTGA", "fmax": "939", "accession": "MN464149.1", "fmin": "528", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "QHR93773.1", "sequence": "MLSGMNHLTLAVQSLERSVSFYKDTLGFRLAARWKNGAYLELGDLWLCLSLDDKRSAQPWPEYTHYAFSALEQDFSSFVAKLIQKGVVEWKKNRSEGNSFYFLDPDGHKLEVHVGNLESRLKQCRVHPYTDMEIFD"}}}}, "ARO_category": {"35944": {"category_aro_name": "fosfomycin", "category_aro_cvterm_id": "35944", "category_aro_accession": "0000025", "category_aro_class_name": "Drug Class", "category_aro_description": "Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction."}, "36272": {"category_aro_name": "fosfomycin thiol transferase", "category_aro_cvterm_id": "36272", "category_aro_accession": "3000133", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin."}, "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."}}, "ARO_name": "FosL1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43215", "model_name": "FosL1", "model_type_id": "40292"}, "3766": {"model_id": "3766", "ARO_accession": "3005027", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-4 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.", "model_sequences": {"sequence": {"6056": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGCCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGAATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACCCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGCGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATAAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTGTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGGAGTACTAAATAA", "fmax": "885", "accession": "LC178555.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645", "NCBI_taxonomy_cvterm_id": "36926"}, "protein_sequence": {"accession": "BAX00166.1", "sequence": "MFFFKKSASTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAISLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGLYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43218", "model_name": "FRI-4", "model_type_id": "40292"}, "3767": {"model_id": "3767", "ARO_accession": "3005028", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-5 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.", "model_sequences": {"sequence": {"6057": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTCTTTGCAAAAAAACAAGCATTATGTCTTTTCTGCTCTGCCTTTCTTTTATTTCATTTAACTCGCTTGCCACTCAGGAAAATAATAGTGTTGCTAAAATGAAGGAACTGGAGACTGCTTTCGGTGGTCGGATAGGTGTTTATCTTTTAAATACAGGGAATGGGAAAGAGTTTTCCTACAGACAGGATGAGAGATTTCCTTTGTGCAGTTCATTTAAGGTGTTTCTCGCTGCATCGGTGTTAAAAAGAATCCAGAGCAAATCTATTTCTCTTGATGATTCGGTGGAGTATGTCGGTCGTGTTATGGAAAAACATTCTCCTGTATCAGAAAAATATCGTGAAAAGGGAGCAAGCGTGCAGACTTTGGCTATGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAACCTGTTAATGGAAAGATACATCGGAGGTCCTGAAGGTTTAACTGCATTTATGCGGTCGACGGGAGATACTGACTTCAGGCTTGATCGCTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGACACATCCACTCCGAAAGCAGTAGCAATGAGCCTTAAAAATATTGCATTTGGTTCGATACTTAATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAGTCAGAGCAGCTGTTCCAGATAAATGGGTTGTTGGCGATAAAACAGGTACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCAGACAACAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTCCTAATCAAAACGACAAGCATGATGAAACAGTAATTAAAAATGCCGCAAAAATAGCTATAGATTCGGTATATGGAAGTTATAAATGA", "fmax": "891", "accession": "MH208723.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae complex sp.", "NCBI_taxonomy_id": "2027919", "NCBI_taxonomy_cvterm_id": "43220"}, "protein_sequence": {"accession": "AWA42532.1", "sequence": "MFLCKKTSIMSFLLCLSFISFNSLATQENNSVAKMKELETAFGGRIGVYLLNTGNGKEFSYRQDERFPLCSSFKVFLAASVLKRIQSKSISLDDSVEYVGRVMEKHSPVSEKYREKGASVQTLAMAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSILNAKNKALLQDWLKGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDNNSPAVIAVYTTRPNQNDKHDETVIKNAAKIAIDSVYGSYK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43219", "model_name": "FRI-5", "model_type_id": "40292"}, "3826": {"model_id": "3826", "ARO_accession": "3005093", "model_param": {"blastp_bit_score": {"param_value": "530", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-899 is a class D beta-lactamase and part of the OXA family. It confers resistance to B-lactams and was originally found in Ralstonia pikettii.", "model_sequences": {"sequence": {"6126": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAACGCCGCCACGCCGCCACCGGCGCCCTGCTTGCTGCGCTTGCAACCTTTGCCCACGCCGAGCACCCGATCTGCACGATCGTGGCCGATGGCGCGACGGGCAAGGCAGTCTTGCAAGAAGGCAGGTGCGACGAGCGCGTGACCCCCGCTTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTTTGACCACGGCTTCCTGAAAGACGAGCACACCCCGGTGGAGCACTTCAGGCACGGTGACCCCGACTGGGGCGGCGAGGCTTGGCACCAGCCGATCGACCCGGCGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCGCAGCGCATTACGCATGCGATGGGCGCGCAGACCTTCCAGGCCTACGTGCGCAAGCTCGGCTACGGCAACATGGATGTGAGCGGCGATCCGGGCAAGAACAACGGCATGGACCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCGGAGGAGCAAGTCGGCTTCATGCGCAGGATCGTCAACCGGCAGTTGCCGGTGTCGGCGCGCACCTACGAGATGGTCGACCGTACCGTGCAGACCTGGCAGGTGCCGGGCGGCTGGTCAGTGCACGGCAAGACGGGCACCGCCGGCCCTGCGCCGGGCAATACCTCGCCCGATGGCACGTGGGACCAGGCGCACGCTTACGGGTGGTTTGTCGGCTGGGCCAGGAAGGGCGACAAGACGTACGTGTTTGCCAACCTGATCCAGGACGACAAGGTTGAGCCGACCTCGGGCGGCATCCGCTCGCGCGATGCGCTGCTTGCGCGCCTGCCCGAAGTGCTTGCCTTTGCCGGGCAATGA", "fmax": "828", "accession": "MN968729.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Ralstonia pickettii", "NCBI_taxonomy_id": "329", "NCBI_taxonomy_cvterm_id": "36921"}, "protein_sequence": {"accession": "QHT72949.1", "sequence": "MMKRRHAATGALLAALATFAHAEHPICTIVADGATGKAVLQEGRCDERVTPASTFKLALAVMGFDHGFLKDEHTPVEHFRHGDPDWGGEAWHQPIDPALWLKYSVVWYSQRITHAMGAQTFQAYVRKLGYGNMDVSGDPGKNNGMDRSWITSSLKISPEEQVGFMRRIVNRQLPVSARTYEMVDRTVQTWQVPGGWSVHGKTGTAGPAPGNTSPDGTWDQAHAYGWFVGWARKGDKTYVFANLIQDDKVEPTSGGIRSRDALLARLPEVLAFAGQ"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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-899", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43306", "model_name": "OXA-899", "model_type_id": "40292"}, "3769": {"model_id": "3769", "ARO_accession": "3005030", "model_param": {"blastp_bit_score": {"param_value": "610", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-7 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.", "model_sequences": {"sequence": {"6059": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAAGTGCACGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTTGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATGAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTACTAAATAA", "fmax": "56649", "accession": "AP019534.1", "fmin": "55764", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645", "NCBI_taxonomy_cvterm_id": "36926"}, "protein_sequence": {"accession": "BBI97867.1", "sequence": "MFFFKKSARTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-7", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43222", "model_name": "FRI-7", "model_type_id": "40292"}, "3818": {"model_id": "3818", "ARO_accession": "3005083", "model_param": {"blastn_bit_score": {"param_value": "5000", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including 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 a specific gene amongst a batch of submitted sequences."}, "snp": {"param_type": "single resistance variant", "param_value": {"9965": "G2061A", "9966": "G2061U", "9967": "A2451U", "9970": "U2504G", "9968": "C2452U", "9969": "U2500A"}, "clinical": {"9965": "G2061A", "9966": "G2061U", "9967": "A2451U", "9970": "U2504G", "9968": "C2452U", "9969": "U2500A"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Mutations in the 23s rRNA of Thermus thermophilus confers resistance to pleuromutilin antibiotics such as tiamulin.", "model_sequences": {"sequence": {"6116": {"dna_sequence": {"partial": "1", "sequence": "GTCAAGATGGTAAGGGCCCACGGTGGATGCCTCGGCACCCGAGCCGATGAAGGACGTGGCTACCTGCGATAAGCCAGGGGGAGCCGGTAGCGGGCGTGGATCCCTGGATGTCCGAATGGGGGAACCCGGCCGGCGGGAACGCCGGTCACCGCGCTTTTTGCGCGGGGGGAACCTGGGGAACTGAAACATCTCAGTACCCAGAGGAGAGGAAAGAGAAATCGACTCCCTGAGTAGCGGCGAGCGAAAGGGGACCAGCCTAAACCGTCCGGCTTGTCCGGGCGGGGTCGTGGGGCCCTCGGACACCGAATCCCCAGCCTAGCCGAAGCTGTTGGGAAGCAGCGCCAGAGAGGGTGAAAGCCCCGTAGGCGAAAGGTGGGGGGATAGGTGAGGGTACCCGAGTACCCCGTGGTTCGTGGAGCCATGGGGGAATCTGGGCGGACCACCGCCTAAGGCTAAGTACTCCGGGTGACCGATAGCGCACCAGTACCGTGAGGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAATAGAGCCTGAAACCGTGGGCTTACAAGCAGTCACGGCCCCGCAAGGGGTTGTGGCGTGCCTATTGAAGCATGAGCCGGCGACTCACGGTCGTGGGCGAGCTTAAGCCGTTGAGGCGGAGGCGTAGGGAAACCGAGTCCGAACAGGGCGTCTAGTCCGCGGCCGTGGACCCGAAACCGGGCGAGCTAGCCCTGGCCAGGGTGAAGCTGGGGTGAGACCCAGTGGAGGCCCGAACCGGTGGGGGATGCAAACCCCTCGGATGAGCTGGGGCTAGGAGTGAAAAGCTAACCGAGCCCGGAGATAGCTGGTTCTCCCCGAAATGACTTTAGGGTCAGCCTCAGGCGCTGACTGGGGCCTGTAGAGCACTGATAGGGCTAGGGGGCCCACCAGCCTACCAAACCCTGTCAAACTCCGAAGGGTCCCAGGTGGAGCCTGGGAGTGAGGGCGCGAGCGATAACGTCCGCGTCCGAGCGCGGGAACAACCGAGACCGCCAGCTAAGGCCCCCAAGTCTGGGCTAAGTGGTAAAGGATGTGGCGCCGCGAAGACAGCCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAGTGCGTAATAGCTCACTGGTCGAGTGGCGCCGCGCCGAAAATGATCGGGGCTCAAGCCCAGCGCCGAAGCTGCGGGTCTGGGGGATGACCCCAGGCGGTAGGGGAGCGTTCCCGATGCCGATGAAGGCCGACCCGCGAGGGCGGCTGGAGGTAAGGGAAGTGCGAATGCCGGCATGAGTAACGATAAAGAGGGTGAGAATCCCTCTCGCCGTAAGCCCAAGGGTTCCTACGCAATGGTCGTCAGCGTAGGGTTAGGCGGGACCTAAGGTGAAGCCGAAAGGCGTAGCCGAAGGGCAGCCGGTTAATATTCCGGCCCTTCCCGCAGGTGCGATGGGGGGACGCTCTAGGCTAGGGGGACCGGAGCCATGGACGAGCCCGGCCAGAAGCGCAGGGTGGGAGGTAGGCAAATCCGCCTCCCAAAAGCTCTGCGTGGTGGGGAAGCCCGTACGGGTGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCTCTAAGCACAACCTGCGGGAACCCGTACCGCAAACCGACACAGGTGGGCGGGTGCAAGAGCACTCAGGCGCGCGGGAGAACCCTCGCCAAGGAACTCTGCAAGTTGGCCCCGTAACTTCGGGAGAAGGGGTGCTCCCTGGGGTGATGAGCTCCGGGGAGCCGCAGTGAACAGGCTCTGGCGACTGTTTACCAAAAACACAGCTCTCTGCGAACTCGTAAGAGGAGGTATAGGGAGCGACGCTTGCCCGGTGCCGGAAGGTCAAGGGGAGGGGTGCAAGCCCCGAACCGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAAAAGCGTAACGACCGGAGCGCTGTCTCGGCGAGGGACCCGGTGAAATTGAACTGGCCGTGAAGATGCGGCCTACCCGTGGCAGGACGAAAAGACCCCGTGGAGCTTTACTGCAGCCTGGTGTTGGCTCTTGGTCGCGCCTGCGTAGGATAGGTGGGAGCCTGTGAACCCCCGCCTCCGGGTGGGGGGGAGGCGCCGGTGAAATACCACCCTGGCGCGGCTGGGGGCCTAACCCTCGGATGGGGGGACAGCGCTTGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTCCCCTCAGGCGGGACGGAAATCCGCCGGAGAGCGCAAGGGTAGAAGGGGGCCTGACTGCGAGGCCTGCAAGCCGAGCAGGGGCGAAAGCCGGGCCTAGTGAACCGGTGGTCCCGTGTGGAAGGGCCATCGATCAACGGATAAAAGTTACCCCGGGGATAACAGGCTGATCTCCCCCGAGCGTCCACAGCGGCGGGGAGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGAAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCACGGGCGCAGGAGGCTTGAGGGGGGCTCTTCCTAGTACGAGAGGACCGGAAGGGACGCACCTCTGGTTTCCCAGCTGTCCCTCCAGGGGCATAAGCTGGGTAGCCATGTGCGGAAGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCCGCCCCAAGATGAGGCCTCCCACGGCGTCAAGCCGGTAAGGACCCGGGAAGACGACCCGGTGGATGGGCCGGGGGTGTAAGCGCCGCGAGGCGTTGAGCCGACCGGTCCCAATCGTCCGAGGTCTTGACCCCTCC", "fmax": "1537382", "accession": "AE017221.1", "fmin": "1534489", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Thermus thermophilus HB27", "NCBI_taxonomy_id": "262724", "NCBI_taxonomy_cvterm_id": "43290"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "ARO_category": {"41330": {"category_aro_name": "23S rRNA with mutation conferring resistance to pleuromutilin antibiotics", "category_aro_cvterm_id": "41330", "category_aro_accession": "3004178", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Point mutations in the 23S rRNA subunit may confer resistance to pleuromutilin 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."}, "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."}}, "ARO_name": "Thermus thermophilus 23s rRNA conferring resistance to pleuromutilin antibiotics", "model_type": "rRNA gene variant model", "model_description": "The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.", "ARO_id": "43292", "model_name": "Thermus thermophilus 23s rRNA conferring resistance to pleuromutilin antibiotics", "model_type_id": "40295"}, "3819": {"model_id": "3819", "ARO_accession": "3005084", "model_param": {"blastp_bit_score": {"param_value": "310", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "dfrA31 is an antibiotic resistance dihydrofolate reductase from an integron found from Vibrio cholerae.", "model_sequences": {"sequence": {"6118": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATATCCATTATGGCAGCAGTTTCTGAGAATGGAGTAATTGGCTCTGGATTGGATATACCTTGGCATGTACAAGGTGAGCAGCTCCTGTTCAAAGCTATGACTTACAATCATTGGCTTTTAGTCGGTCGTAAAACTTTCGACTCAATGGGTAAACTTCCCAATAGGAAATATGCTGTGGTTACTCGCTCAGAAATGGTCTCGAATGATCCAGATGTTATTTATTTCACCAGCATTGAATCGGCATTATCTTACTTAGACAATACGACAACACATGTCTTTGTTTCTGGTGGTGGTGAAATTTACAAAGCATTAATCGAACAAGCAGATGTTATCCATCTTTCAGTGATTCATAAGCACATCTCTGGCGACGTGTTTTTCCCTTCAGTTCCACAGAGTTTCAAACAAACATTTGAGCAAAGTTTCAGTTCAAATATTGATTACACGTACCAAATTTGGGCAAAGGGCTAA", "fmax": "2305", "accession": "AB200915.1", "fmin": "1831", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae O1", "NCBI_taxonomy_id": "127906", "NCBI_taxonomy_cvterm_id": "43295"}, "protein_sequence": {"accession": "BAD88719.1", "sequence": "MKISIMAAVSENGVIGSGLDIPWHVQGEQLLFKAMTYNHWLLVGRKTFDSMGKLPNRKYAVVTRSEMVSNDPDVIYFTSIESALSYLDNTTTHVFVSGGGEIYKALIEQADVIHLSVIHKHISGDVFFPSVPQSFKQTFEQSFSSNIDYTYQIWAKG"}}}}, "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": "dfrA31", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43294", "model_name": "dfrA31", "model_type_id": "40292"}, "3758": {"model_id": "3758", "ARO_accession": "3005015", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Vibrio metallo-B-lactamase 1, also known as VMB-1, is carbapenemase beta-lactamase that is found in plasmid pVB1796 from Vibrio alginolyticus.", "model_sequences": {"sequence": {"6048": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGTATATTATTCTATTCCTTCTCTTGATTCCTTCTATTGTATTTGCAAACAACGAAGGCACTAAAGAACTTAAATTAAAAAAGTTAAGTGATAACGTTTATCAACATATTTCATATAAGAGGGTTGAGCCATGGGGTTTAATTGGAGCCTCAGGCTTAGTTGTTATTAATGGCACTGAAGCACATATGATTGATACACCTTGGACAACCCAAGGAACAAAACAACTAATTGAATGGATTGAGGCTAAAGGTCTAACTATAAAAAGTGCAGTAGTTACGCATTTTCATGAGGATGCTAGTGGTGATATACCACTTTTAAATGATTTGAAAATAAAAACGTATGCAACATCACTAACTAATAAGCTTCTTAAATTAAACCAAAAAGAAGTGTCTAGTGATGAAATATCAAGTAATACCTTTGAATTTATTGATGGTGTTGCTAGTGTATTTTATCCCGGAGCGGGGCATACAGAGGATAATATTGTTGTTTGGCTACCTAATGAAAAGATATTGTTTGGAGGTTGTTTTGTAAAAAGCCTTAAGAATAAAAATTTAGGTTATACAGGCGACGCAAATATTAGTGAATGGCCAAACTCTATGCAAAAAGTCATTAATCGTTATCCTGATGCCAAATTAGTTGTTCCAGGACATGGTGAAGTCGGAGATGTTAGCTTACTGAAGCATACTCAAGCATTAGCTTTGTCTGCAGCGGCCTCTAACAAGAAAATCAACAAGGACTAA", "fmax": "756", "accession": "MN719868.1", "fmin": "12", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio alginolyticus", "NCBI_taxonomy_id": "663", "NCBI_taxonomy_cvterm_id": "43205"}, "protein_sequence": {"accession": "QGQ32905.1", "sequence": "MKYIILFLLLIPSIVFANNEGTKELKLKKLSDNVYQHISYKRVEPWGLIGASGLVVINGTEAHMIDTPWTTQGTKQLIEWIEAKGLTIKSAVVTHFHEDASGDIPLLNDLKIKTYATSLTNKLLKLNQKEVSSDEISSNTFEFIDGVASVFYPGAGHTEDNIVVWLPNEKILFGGCFVKSLKNKNLGYTGDANISEWPNSMQKVINRYPDAKLVVPGHGEVGDVSLLKHTQALALSAAASNKKINKD"}}}}, "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."}, "43203": {"category_aro_name": "VMB beta-lactamase", "category_aro_cvterm_id": "43203", "category_aro_accession": "3005014", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Vibro metallo-B-lactamase, also known as VMB is a carbapenemase beta-lactamase gene family."}, "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."}}, "ARO_name": "VMB-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43204", "model_name": "VMB-1", "model_type_id": "40292"}, "3754": {"model_id": "3754", "ARO_accession": "3005009", "model_param": {"blastp_bit_score": {"param_value": "190", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "QacE is a resistance gene conferring resistance to antiseptics.", "model_sequences": {"sequence": {"6044": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTATGAAATCCATCCCTGTCGGTGTTGCTTATGCACTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTTTTAAACTTGCTTTCCAAAGCAAGTGCCCACTAA", "fmax": "5507", "accession": "HQ730118.1", "fmin": "5174", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AEH26330.1", "sequence": "MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVMKSIPVGVAYALWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIVSGVVVLNLLSKASAH"}}}}, "ARO_category": {"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."}, "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": "qacE", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43197", "model_name": "qacE", "model_type_id": "40292"}, "3817": {"model_id": "3817", "ARO_accession": "3005081", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}, "snp": {"param_type": "single resistance variant", "param_value": {"9964": "R144H", "9963": "R144C"}, "clinical": {"9964": "R144H", "9963": "R144C"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Thermus thermophilus ribosomal protein uL3 containing various mutations conferring resistance to tiamulin. Mutations in the ribosomal protein of uL3 acts by interfering with local rRNA conformation thus conferring resistance.", "model_sequences": {"sequence": {"6113": {"dna_sequence": {"partial": "0", "sequence": "GTGAAGGGCATCTTGGGCGTCAAGGTGGGCATGACCCGCATCTTCCGCGACGACCGCGCCGTCCCCGTCACGGTCATCCTTGCGGGGCCGTGCCCCGTGGTGCAGCGCCGCACCCCGGAGAAGGACGGCTACACCGCGGTGCAGCTGGGCTTCCTTCCCCAAAACCCCAAGCGGGTGAACCGCCCCCTTAAGGGGCACTTCGCCAAGGCCGGGGTGGAGCCCGTGCGCATCCTGCGGGAGATCCGGGACTTCAACCCCGAAGGCGACACGGTCACGGTGGAGATCTTCAAGCCCGGGGAGCGCGTGGACGTGACGGGCACCTCCAAGGGCCGGGGCTTCGCCGGCGTGATGAAGCGCTGGAACTTCGCGGGCGGCCCCGACTCCCACGGCGCCCACAAGATCCACCGCCACCCCGGCTCCATCGGGAACCGCAAGACCCCCGGTCGCGTCTACAAGGGCAAGAAGATGGCGGGCCACTACGGGGCCGAGCGCGTGACGGTCATGAACCTCGAGGTGGTGGACGTCATCCCCGAGGAGAACCTGCTTTTGGTCAAGGGGGCCGTCCCCGGTCCCAACGGCGGCCTGGTCATCGTCCGCGAGACCAAGAAGGCGGCCAAGTGA", "fmax": "1266643", "accession": "AE017221.1", "fmin": "1266022", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Thermus thermophilus HB27", "NCBI_taxonomy_id": "262724", "NCBI_taxonomy_cvterm_id": "43290"}, "protein_sequence": {"accession": "AAS81670.1", "sequence": "MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKAAK"}}}}, "ARO_category": {"43291": {"category_aro_name": "Ribosomal protein mutation conferring resistance to pleuromutilin antibiotics", "category_aro_cvterm_id": "43291", "category_aro_accession": "3005082", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Ribosomal protein mutations that interfere with the rRNA conformation at the active site thus conferring antibiotic 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."}, "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."}}, "ARO_name": "Thermus thermophilus uL3 mutations conferring resistance to pleuromutilin antibiotics", "model_type": "protein variant model", "model_description": "The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.", "ARO_id": "43289", "model_name": "Thermus thermophilus uL3 mutations conferring resistance to pleuromutilin antibiotics", "model_type_id": "40293"}, "3800": {"model_id": "3800", "ARO_accession": "3005060", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "A class D OXA-like beta-lactamase described in the emerging pathogen Cupriavidus gilardii", "model_sequences": {"sequence": {"6095": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGTCCCGTACCGAAGCGCAGTCCCTGCACGCGCATGGCCTGTATCGCCGCCGCCTGCTGCAACTGGCCGGCGGCGCCGCGCTGCTGCCTGCCGCGCGCCTGGCGCTGGCCGATGTCGCGCCGGCAAGCGCCGTCGCCGCGCCGAGCGAAGTCGCCCGCGGTGATTTGATGTCGCACTTTCGCGCGCTGGACGTCGACGGCTGTTTTGCGCTGTTCGACGTCAAGGCGAACCGGATGACGCTGGTCAACGCATCGCGTGCGAAGACGCGCATGGTGCCGGCGTCGACCTACAAGATTCCGAACAGCCTGATCGCCTTCGAGACCGGCGTGGTGGCCGATCCGGACCAGATCCAGCCATATGGCGGCGGCAAGACGCGCTTCCCGCAGTGGCAGCGCGACATGAATCTGCGCGAGGCGATCGCGATGTCGAATGTGCCGGTCTACCAGGGCATTGCCCGGCGGATCGGCATGCAGCGGATGCAGACGTGGGTCGACCGGCTCGACTATGGCAACCGGCAACTCGGGAAGGTGGTGGATCAGTTCTGGCTGCGCGGGCCGCTGGCGATCTCGGCGGCCGAACAGACGCGCTTTCTGGCGCGGCTGGCACAGGGCCAACTACCGGCGTCGCGCCTGAGCCAGCAATGGGTGCGCGAGATCCTGCGCGTCGAAGCCAATGACGATCACGCGATCTACGCCAAGACGGGCTGGGCGATGGATGCCGGGCTGAACCACGGCTGGTGGGTGGGGTGGGTCGAACGCAGCGGCGGCGTCCATGCCTTCGCGCTCAATATGGATCTGCAGCGCGAGGAACTGGCGCCAAAGCGCATGGCCATCGCACGGGCGATGATGGCGGAACTTGGCGTGTTGCCCGTGGAGAACGGGCAAGCGCGCAAGATGAGCTAG", "fmax": "906", "accession": "MN313890.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Cupriavidus gilardii", "NCBI_taxonomy_id": "82541", "NCBI_taxonomy_cvterm_id": "43264"}, "protein_sequence": {"accession": "QEE23059.1", "sequence": "MKSRTEAQSLHAHGLYRRRLLQLAGGAALLPAARLALADVAPASAVAAPSEVARGDLMSHFRALDVDGCFALFDVKANRMTLVNASRAKTRMVPASTYKIPNSLIAFETGVVADPDQIQPYGGGKTRFPQWQRDMNLREAIAMSNVPVYQGIARRIGMQRMQTWVDRLDYGNRQLGKVVDQFWLRGPLAISAAEQTRFLARLAQGQLPASRLSQQWVREILRVEANDDHAIYAKTGWAMDAGLNHGWWVGWVERSGGVHAFALNMDLQREELAPKRMAIARAMMAELGVLPVENGQARKMS"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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."}, "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-837", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43263", "model_name": "OXA-837", "model_type_id": "40292"}, "3803": {"model_id": "3803", "ARO_accession": "3005063", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cprR is one part of a two-component regulatory system. It with its counterpart cprS induce the Arn operon to confer resistance to peptide antibiotics.", "model_sequences": {"sequence": {"6098": {"dna_sequence": {"partial": "0", "sequence": "ATGCATATCCACGTACTCGTCGTCGAAGACAACTTCGATCTCGCCGGCACCGTCATCGACTACCTCGAGGCCGCCGGGGTGGTCTGCGATCACGCCCGCGACGGCCAGGCCGGCCTCAACCTGGCGCGCGCCAACCGCTACGACGTGATCCTGCTGGACATCATGCTGCCGCGCATCAACGGCCGGCAGGTCTGTCGCCAGCTGCGCGAAGCCGGCCTGCAGACCCCGGTACTCATGCTCACCGCCCTGGATACCCTGCAGGACAAGCTCGACGGCTTCGACGCCGGCGCCGACGACTACCTGCTCAAGCCCTTCGAACTGCCGGAGCTGCTGGTCCGCCTGCAAGCCCTCAGCCGGCGCCGCAGCGGCCAGGCCCAGCGCCTGCAGGTCGACGACCTGGTGATGGACCTCGACAGCCGCCAGGCCAGCCGCGGCGGCACGCCCCTGGCGCTGTCCCCCACCGCCTGGAAGATCCTTGAGTGCCTGATGCGCGCCAGCCCCGCGCTGGTCACCCGCGAGCAGCTGGGGCGCAGCGTCTGGGGCGACGAACCGCCGGAAAGCAACACCCTCAACGTGCACATGCACCACCTGCGCAGCACCGTCGACAAGGGGTTCGCCACCCCTCTGATCCATACCCTGCACAGCGTCGGCTTCCAGCTGGAGCGCAAATGA", "fmax": "3451509", "accession": "AE004091.2", "fmin": "3450837", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "AAG06465.1", "sequence": "MHIHVLVVEDNFDLAGTVIDYLEAAGVVCDHARDGQAGLNLARANRYDVILLDIMLPRINGRQVCRQLREAGLQTPVLMLTALDTLQDKLDGFDAGADDYLLKPFELPELLVRLQALSRRRSGQAQRLQVDDLVMDLDSRQASRGGTPLALSPTAWKILECLMRASPALVTREQLGRSVWGDEPPESNTLNVHMHHLRSTVDKGFATPLIHTLHSVGFQLERK"}}}}, "ARO_category": {"41433": {"category_aro_name": "pmr phosphoethanolamine transferase", "category_aro_cvterm_id": "41433", "category_aro_accession": "3004269", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane."}, "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."}, "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."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "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": "cprR", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43267", "model_name": "cprR", "model_type_id": "40292"}, "3813": {"model_id": "3813", "ARO_accession": "3005077", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-7 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.", "model_sequences": {"sequence": {"6108": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTCTGTTCTTTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "1199", "accession": "KJ910995.1", "fmin": "281", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AIW80572.1", "sequence": "MLNKLKIGTLLLLTLTACLPNSVLSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-7", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43284", "model_name": "ROB-7", "model_type_id": "40292"}, "3802": {"model_id": "3802", "ARO_accession": "3005062", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "A novel aminoglycoside 3''-adenyltransferase gene and aminoglycoside resistance gene identified from Cupriavidus gilardii. ANT(3'')-Ib / aadA32 confers resistance to spectinomycin and streptomycin.", "model_sequences": {"sequence": {"6097": {"dna_sequence": {"partial": "0", "sequence": "ATGCCACCGCCTGCGAACGAGCCCGTCCCGGCCGAAGTCCAGCCCATTCTCGATGTCGTGGTCCGCGCGCTGGGTGACGACATCGCCGGCGCGTACCTGTTCGGCTCCGCCATTGCAGGCGGGCTGCGGCCGGACAGCGATGTCGACCTGCTGGTGCTGACGCATCGAACGATGTCCCGGCAGAGCCGCGAGGATCTGGTGGCCGCGTTGATGGAAGTCTCCGGCGCGCGCGCGGGGCGGGGGCCGGCCCGCAATGCCGAGGTCACGGTCGTCGTGCTCGGCGACATCGCCCCGTGGCGCCACCCGGCGCGGAGCGACTTCGTCTACGGCGAATGGCTGCGCGACGATTTCGCAGCGGGCGTGGTGCCGGCGCCGACCGCCGATCCCGATCTGACGCTGGTGCTGGCCACGGCCTTGCAGAGCCACCGCGCATTGATGGGGCCGGGGCTTGCCGAATTTCTCCCCGCGATTCCTTACGCCGATATCCGGCGCGCGATGGCGGACAGCTTGCCGGGGCTGGTGGCCAACGTCCGCGGCGACGAACGCAACGTCATGCTGACGCTGGCCCGCATGTGGGTCACGGTTGCCACGGGCGACATCGTGCCGAAGGACGCGGCGGCCGATTGGCTGCTGCCGCGTCTGCCGCCGGAGCGGCGCGCGTTATTGGCGACGGCGCGCGACGCGTATCGCGGTCATGTCGCCGACGAAGCCTGGCACGAATGTCGGGCCGACGTCAGCGAATGGGTGAGCGAGGTCAGCCAGGCCATCGCGCGAACGCTCCACGACAGCGTCAAGGCATGA", "fmax": "801", "accession": "MN366379.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Cupriavidus gilardii", "NCBI_taxonomy_id": "82541", "NCBI_taxonomy_cvterm_id": "43264"}, "protein_sequence": {"accession": "QEQ43477.1", "sequence": "MPPPANEPVPAEVQPILDVVVRALGDDIAGAYLFGSAIAGGLRPDSDVDLLVLTHRTMSRQSREDLVAALMEVSGARAGRGPARNAEVTVVVLGDIAPWRHPARSDFVYGEWLRDDFAAGVVPAPTADPDLTLVLATALQSHRALMGPGLAEFLPAIPYADIRRAMADSLPGLVANVRGDERNVMLTLARMWVTVATGDIVPKDAAADWLLPRLPPERRALLATARDAYRGHVADEAWHECRADVSEWVSEVSQAIARTLHDSVKA"}}}}, "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."}, "41439": {"category_aro_name": "ANT(3'')", "category_aro_cvterm_id": "41439", "category_aro_accession": "3004275", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Nucleotidylylation of streptomycin at the hydroxyl group at position 3''"}, "35958": {"category_aro_name": "streptomycin", "category_aro_cvterm_id": "35958", "category_aro_accession": "0000040", "category_aro_class_name": "Antibiotic", "category_aro_description": "Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth."}, "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": "ANT(3'')-Ib", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43266", "model_name": "ANT(3'')-Ib", "model_type_id": "40292"}, "3798": {"model_id": "3798", "ARO_accession": "3005057", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Tet(X5) is a tetracycline inactivating enzyme. It is a variant of Tet(X).", "model_sequences": {"sequence": {"6093": {"dna_sequence": {"partial": "0", "sequence": "ATGACAATGCGAATAGATACAGACAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATGAAAAAGGCAATATTTTATCCACAAAAAATGTAAGACCCGAAAATCGTTTTGACAATCCTGAAATAAACAGAAATGACTTAAGGACTATCCTATTAAATAGTTTACAAAATGATACCGTCATTTGGGATAGAAAACTTGTTACCCTTGAACCTGATAAGGAGAAGTGGATACTAACTTTTGAGGATAAATCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCGGAGGTGAACTGTCCTGGATTTTTTCAGCTTTGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAGCAAAACGCGGGTAGATTTTCAAGACAGAAATAGTGTCGTTGATTTTCTCCTGAAAAAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTTTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGATAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGTGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTGCTTATGGAAGAGAAGCACAGGCAGAATCAATAATAAACGAAACGGAAATGTTCAGCCTCGACTTTTCTTTCCAAAAACTAATGAATCTATAA", "fmax": "85964", "accession": "NZ_CP040912.1", "fmin": "84797", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296", "NCBI_taxonomy_cvterm_id": "36787"}, "protein_sequence": {"accession": "WP_150378267.1", "sequence": "MTMRIDTDKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVRPENRFDNPEINRNDLRTILLNSLQNDTVIWDRKLVTLEPDKEKWILTFEDKSSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKSKTRVDFQDRNSVVDFLLKKFSDWDERYKELIRLTSSFVGLATRIFPLDKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFAYGREAQAESIINETEMFSLDFSFQKLMNL"}}}}, "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."}, "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."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}, "ARO_name": "Tet(X5)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43259", "model_name": "Tet(X5)", "model_type_id": "40292"}, "3782": {"model_id": "3782", "ARO_accession": "3005039", "model_param": {"blastp_bit_score": {"param_value": "800", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "PDC-55 is an ambler class C beta-lactamase from Pseudomonas aeruginosa.", "model_sequences": {"sequence": {"6075": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCGCTCGCGAGGGCGACGGAGCGTAG", "fmax": "1215", "accession": "KJ949070.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AIG19992.1", "sequence": "MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKRAREGDGA"}}}}, "ARO_category": {"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."}, "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."}, "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."}}, "ARO_name": "PDC-55", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43237", "model_name": "PDC-55", "model_type_id": "40292"}, "3783": {"model_id": "3783", "ARO_accession": "3005040", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "YajC interacts with the AcrAB-TolC efflux pump in a way that in uncharacterized but is shown to grant increased fitness in the presence of linezolid, rifampicin, and vancomycin.", "model_sequences": {"sequence": {"6076": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCTTTCTAATTCCCGCTGCCTACGCCGACGCAGCCGCTCCGGCAGCCGCTGGCCCGGCCGGCACCGGTTTCGAGTGGGTCTTCCTGGTTGGTTTCCTGGTCATCTTCTACCTGATGATCTGGCGTCCCCAGGCCAAGCGCGCCAAGGAACACAAGAACCTGCTGGGCAACCTGCAAAAAGGTGACGAAGTCGTCACTTCCGGCGGTATCGCCGGCAAGGTGACCAAGGTCGCCGACGATTTCGTCGTCGTCGAGGTCTCCGACAACGTCGAGCTGAAGTTCCAGAAGGCCGCGATTGCCGCGACCCTGCCGAAAGGCACCCTGAAAGCGATCTGA", "fmax": "339", "accession": "VAOQ01003483.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "TKW44661.1", "sequence": "MSFLIPAAYADAAAPAAAGPAGTGFEWVFLVGFLVIFYLMIWRPQAKRAKEHKNLLGNLQKGDEVVTSGGIAGKVTKVADDFVVVEVSDNVELKFQKAAIAATLPKGTLKAI"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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": "Drug Class", "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."}, "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."}, "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."}, "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."}, "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": "YajC", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43238", "model_name": "YajC", "model_type_id": "40292"}, "3780": {"model_id": "3780", "ARO_accession": "3005037", "model_param": {"blastp_bit_score": {"param_value": "780", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ADC-159 is an ADC beta-lactamase and a ambler class C beta-lactamase.", "model_sequences": {"sequence": {"6073": {"dna_sequence": {"partial": "0", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACACCTGGTAAATATTGGGAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA", "fmax": "1152", "accession": "MG229642.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ATP60652.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWEELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}}}}, "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."}, "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."}, "40543": {"category_aro_name": "ADC beta-lactamase without carbapenemase activity", "category_aro_cvterm_id": "40543", "category_aro_accession": "3003846", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis."}}, "ARO_name": "ADC-159", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43235", "model_name": "ADC-159", "model_type_id": "40292"}, "3781": {"model_id": "3781", "ARO_accession": "3005038", "model_param": {"blastp_bit_score": {"param_value": "800", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "PDC-65 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa", "model_sequences": {"sequence": {"6074": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAAAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA", "fmax": "1194", "accession": "KJ949080.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AIG20002.1", "sequence": "MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGKPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"}}}}, "ARO_category": {"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."}, "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."}, "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."}}, "ARO_name": "PDC-65", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43236", "model_name": "PDC-65", "model_type_id": "40292"}, "3786": {"model_id": "3786", "ARO_accession": "3005043", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA9 is a Major Facilitator Superfamily efflux gene that is found in Salmonella enterica.", "model_sequences": {"sequence": {"6079": {"dna_sequence": {"partial": "0", "sequence": "ATGACCACCACACGCCCCGCGTGGGCCTATACGCTGCCGGCAGCCTTGCTGCTTATGGCTCCCTTCGACATCCTCGCCTCGCTGGCGATGGATATTTATCTTCCAGTCGTTCCGGCGATGCCGGGCGTCCTGAACACGACTCCATCCATAATCCAACTCACGTTGAGCCTCTACATGGTGATGCTCGGTGTGGGCCAAGTGATCTTTGGGCCACTCTCCGATCGCGTCGGGCGACGGCCGATCCTGCTTGTAGGCGCAACGGCTTTCGTTGCTGCGTCTCTGGGAGCGGCTTGTTCTTCAACTGCATTAGCCTTTGTTGCGTTTCGTCTGGTTCAGGCTGTTGGAGCATCGGCCATGCTGGTGGCCACCTTCGCGACCGTGCGCGACGTATATGCCAATCGTCCCGAAGGTGCCGTCATCTACGGCCTTTTCAGTTCGATGCTGGCGTTCGTGCCTGCGCTCGGCCCTATAGCCGGTGCGCTGATCGGCGAGTTTTGGGGATGGCAGGCGATCTTCATCACACTGGCTGCACTGGCTTCGCTCGCACTCTTAAACGCCAGTTTCAGGTGGCATGAAACCCGACCGTTGGATCAGGCCAGAACGCAACGATCTGTTTTGCCGATCTTCGCGAGTCCGGCCTTTTGGGTTTACACGGTCGGATTTAGTGCCGGCATGGGCACATTCTTCGTTTTCTTCTCGACAGCCCCCCGTGTTCTCATAGGCCAAGCCGGCTATTCCGAGATCGGATTTAGCTTGGCCTTCGCGACTGTCGCGCTGGTCATGGTCACGACAACCCGCTTCGCAAAGTCCTTCGTTGCCAAATGGGGTATCGCGGGATGCGTAGCGCGCGGGATGGCGTTGCTCGTTTCCGGCGCGATCCTGTTGGGGATCGGCCAACTTTTCGGATCGCCGTCATTTTTCAGCTTCATCCTGCCGATGTGGGTTGTCGCGGTCGGCATTGTCTTCACGGTGTCCGTTACCGCCAACGGCGCACTTGCGCAGTTCGACGACATCGCTGGATCAGCGGTTGCGTTCTACTTCTGCATCCAAAGCCTGATAGTCAGTATCGTCGGGACATTGGCGGTGACGCTGTTAAACGGCGATACAGCGTGGCCCGTGATTTGTTACGCCACGGCAATGGCAGTGCTGGTGTCGTTGGGGCTGGCGCTCCTTCGATCCCGTGATGCTGCCACCGAGAAGTCGCCAGTCGTCTAG", "fmax": "26038", "accession": "AY963803.6", "fmin": "24823", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Salmonella enterica subsp. enterica serovar Emek", "NCBI_taxonomy_id": "286784", "NCBI_taxonomy_cvterm_id": "35796"}, "protein_sequence": {"accession": "ABZ01840.1", "sequence": "MTTTRPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGVLNTTPSIIQLTLSLYMVMLGVGQVIFGPLSDRVGRRPILLVGATAFVAASLGAACSSTALAFVAFRLVQAVGASAMLVATFATVRDVYANRPEGAVIYGLFSSMLAFVPALGPIAGALIGEFWGWQAIFITLAALASLALLNASFRWHETRPLDQARTQRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAGYSEIGFSLAFATVALVMVTTTRFAKSFVAKWGIAGCVARGMALLVSGAILLGIGQLFGSPSFFSFILPMWVVAVGIVFTVSVTANGALAQFDDIAGSAVAFYFCIQSLIVSIVGTLAVTLLNGDTAWPVICYATAMAVLVSLGLALLRSRDAATEKSPVV"}}}}, "ARO_category": {"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."}, "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": "cmlA9", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43241", "model_name": "cmlA9", "model_type_id": "40292"}, "3787": {"model_id": "3787", "ARO_accession": "3005044", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OmpA is a porin that confers resistance to beta-lactam antibiotics.", "model_sequences": {"sequence": {"6080": {"dna_sequence": {"partial": "0", "sequence": "GTGAGGTCTTTTGTAACTTCATGGCGAATTTTGGATGATAATGAGGCGCAAAAAATGAAAAAGACAGCTATCGCGATTGCAGTGGCACTGGCTGGCTTCGCTACCGTAGCGCAGGCCGCTCCGAAAGATAACACCTGGTATGCAGGTGGTAAACTGGGTTGGTCCCAGTATCACGACACCGGTTTCTACGGTAACGGTTTCCAGAACAACAACGGTCCGACCCGTAACGATCAGCTTGGTGCTGGTGCGTTCGGTGGTTACCAGGTTAACCCGTACCTCGGTTTCGAAATGGGTTATGACTGGCTGGGCCGTATGGCATATAAAGGCAGCGTTGACAACGGTGCTTTCAAAGCTCAGGGCGTTCAGCTGACCGCTAAACTGGGTTACCCGATCACTGACGATCTGGACATCTACACCCGTCTGGGCGGCATGGTTTGGCGCGCTGACTCCAAAGGCAACTACGCTTCTACCGGCGTTTCCCGTAGCGAACACGACACTGGCGTTTCCCCAGTATTTGCTGGCGGCGTAGAGTGGGCTGTTACTCGTGACATCGCTACCCGTCTGGAATACCAGTGGGTTAACAACATCGGCGACGCGGGCACTGTGGGTACCCGTCCTGATAACGGCATGCTGAGCCTGGGCGTTTCCTACCGCTTCGGTCAGGAAGATGCTGCACCGGTTGTTGCTCCGGCTCCGGCTCCGGCTCCGGAAGTGGCTACCAAGCACTTCACCCTGAAGTCTGACGTTCTGTTCAACTTCAACAAAGCTACCCTGAAACCGGAAGGTCAGCAGGCTCTGGATCAGCTGTACACTCAGCTGAGCAACATGGATCCGAAAGACGGTTCCGCTGTTGTTCTGGGCTACACCGACCGCATCGGTTCCGAAGCTTACAACCAGCAGCTGTCTGAGAAACGTGCTCAGTCCGTTGTTGACTACCTGGTTGCTAAAGGCATCCCGGCTGGCAAAATCTCCGCTCGCGGCATGGGTGAATCCACCCCGGTTACTGGCAACACCTGTGACAACGTGAAAGCTCGCGCTGCCCTGATCGATTGCCTGGCTCCGGATCGTCGTGTAGAGATCGAAGTTAAAGGCTACAAAGAAGTTGTAACTCAGCCGGCGGCTTAA", "fmax": "2175099", "accession": "FO834906.1", "fmin": "2173974", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "CDO13836.1", "sequence": "MRSFVTSWRILDDNEAQKMKKTAIAIAVALAGFATVAQAAPKDNTWYAGGKLGWSQYHDTGFYGNGFQNNNGPTRNDQLGAGAFGGYQVNPYLGFEMGYDWLGRMAYKGSVDNGAFKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADSKGNYASTGVSRSEHDTGVSPVFAGGVEWAVTRDIATRLEYQWVNNIGDAGTVGTRPDNGMLSLGVSYRFGQEDAAPVVAPAPAPAPEVATKHFTLKSDVLFNFNKATLKPEGQQALDQLYTQLSNMDPKDGSAVVLGYTDRIGSEAYNQQLSEKRAQSVVDYLVAKGIPAGKISARGMGESTPVTGNTCDNVKARAALIDCLAPDRRVEIEVKGYKEVVTQPAA"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "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."}, "41445": {"category_aro_name": "General Bacterial Porin with reduced permeability to beta-lactams", "category_aro_cvterm_id": "41445", "category_aro_accession": "3004281", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein."}, "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": "OmpA", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43242", "model_name": "OmpA", "model_type_id": "40292"}, "3784": {"model_id": "3784", "ARO_accession": "3005041", "ARO_description": "mlaF from the mla system is a gene proposed to play a part in the transport of phospholipids to the outer membrane. Insertions in mlaF are shown to confer resistance to linezolid.", "model_sequences": {"sequence": {"6077": {"dna_sequence": {"partial": "0", "sequence": "ATGGAGCAGTCTGTGGCGAATTTAGTCGATATGCGCGATGTCAGTTTTACGCGTGGCAATCGCTGCATCTTCGATAATATTTCCCTGACCGTGCCGCGAGGGAAGATCACGGCGATCATGGGGCCATCGGGCATCGGTAAAACGACGCTACTCCGTCTGATTGGCGGGCAAATCGCACCAGATCATGGTGAGATCCTTTTCGATGGTGAGAATATTCCGGCGATGTCTCGTTCGCGCCTGTATACAGTGCGCAAACGGATGAGCATGTTATTTCAGTCCGGGGCGTTGTTCACTGATATGAACGTATTTGACAACGTCGCCTATCCACTGCGGGAACATACCCAACTTCCCGCACCATTGTTGCATAGTACGGTGATGATGAAGCTGGAGGCCGTGGGGCTGCGTGGAGCGGCTAAACTTATGCCTTCTGAACTTTCCGGTGGGATGGCGCGGCGTGCAGCGCTGGCACGTGCGATTGCGCTGGAGCCGGATCTCATCATGTTTGATGAGCCCTTTGTTGGGCAAGATCCCATTACCATGGGCGTGCTGGTGAAGCTGATTTCTGAGCTGAACAGCGCGCTGGGCGTGACTTGTGTGGTGGTTTCTCACGATGTGCCGGAAGTGTTAAGTATTGCGGATCACGCCTGGATCCTGGCGGACAAAAAAATTGTCGCTCATGGCAGTGCCCAGGCGTTGCAGGCGAATCCTGATCCGCGCGTACGTCAGTTTCTGGACGGGATAGCTGACGGGCCTGTTCCGTTCCGCTATCCTGCCGGCGATTATCACGCTGATCTTTTACCAGGGAGTTAA", "fmax": "3995580", "accession": "LR730402.1", "fmin": "3994770", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "VWQ04088.1", "sequence": "MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAPDHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPLLHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITMGVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRVRQFLDGIADGPVPFRYPAGDYHADLLPGS"}}}}, "ARO_category": {"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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "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": "mlaF", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "43239", "model_name": "mlaF", "model_type_id": "40354"}, "3785": {"model_id": "3785", "ARO_accession": "3005042", "ARO_description": "mlaD from the mla system is a gene proposed to play a part in the transport of phospholipids to the outer membrane. Insertions in mlaD are shown to confer resistance to linezolid.", "model_sequences": {"sequence": {"6078": {"dna_sequence": {"partial": "0", "sequence": "ATGCAAACGAAAAAAAATGAAATTTGGGTGGGTATCTTTTTATTAGCAGCACTGCTTGCGGCGCTGTTTGTTTGCCTGAAGGCAGCGAACGTGACGTCTATACGTACTGAACCGACCTATACGCTTTATGCGACGTTCGATAACATTGGCGGCCTGAAAGCCCGCTCTCCGGTCAGCATTGGTGGCGTTGTTGTGGGCCGGGTGGCGGATATTACGCTGGACCCGAAAACCTATCTGCCGCGCGTAACGCTGGAAATTGAACAACGTTATAACCACATTCCTGATACCAGTTCGCTGAGCATTCGTACTTCCGGCCTGCTGGGGGAACAATATCTGGCATTAAACGTCGGTTTTGAAGACCCGGAACTGGGGACTGCTATCCTGAAGGATGGCGATACAATTCAGGACACCAAGTCTGCGATGGTGCTGGAAGATCTCATTGGTCAGTTCCTTTACGGTAGTAAAGACGATGACAATAAGAATAGTGGCGATGCGCCAGCTGCTGCGCCAGGTAATAATGAAACCACTGAACCTGTGGGTACAACGAAATAA", "fmax": "3996926", "accession": "LR730402.1", "fmin": "3996374", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "VWQ04090.1", "sequence": "MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSIGGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFEDPELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKDDDNKNSGDAPAAAPGNNETTEPVGTTK"}}}}, "ARO_category": {"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."}, "36002": {"category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_cvterm_id": "36002", "category_aro_accession": "0010001", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes."}, "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": "mlaD", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "43240", "model_name": "mlaD", "model_type_id": "40354"}, "3768": {"model_id": "3768", "ARO_accession": "3005029", "model_param": {"blastp_bit_score": {"param_value": "610", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-6 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.", "model_sequences": {"sequence": {"6058": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTTGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTTGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATGAGTCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGGAGTACTAAATAA", "fmax": "885", "accession": "MK248729.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "AZK35806.1", "sequence": "MFFFKKSASTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"}}}}, "ARO_category": {"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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}}, "ARO_name": "FRI-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43221", "model_name": "FRI-6", "model_type_id": "40292"}, "3788": {"model_id": "3788", "ARO_accession": "3005045", "model_param": {"blastp_bit_score": {"param_value": "350", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "SatA is part of the Streptothricin acetyltransferase gene family. It confers resistance to nucleoside antibiotics.", "model_sequences": {"sequence": {"6081": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCCTTTTAATTAGAGAGTTAGAAACAAATGATTTAGATAATTTCCCGGAGATTGATGACAGTTTTATAGTGAATGCTCGGTTAATGCTTTCTCTTTCAAAAGTAAATAGACGCATAGAATATACAGTAGAAGACGTTCCGAGTTATGAAAAAAGTTATTTACAAAATGATAATGAAGAACTGGTGTACAATGAATATATAAATAAGCCAAATCAAATAATTTACATAGCACTGTTACATAACCAAATTATTGGATTCATAGTATTGAAAAAGAATTGGAATAACTATGCTTACATAGAAGATATAACGGTGGATAAAAAATATCGTACACTCGGGGTTGGTAAAAGATTAATTGCTCAAGCAAAACAGTGGGCAAAAGAAGGCAACATGCCAGGTATCATGCTTGAAACGCAAAATAATAATGTCGCAGCATGTAAGTTCTATGAAAAATGCGGATTTGTAATTGGTGGATTTGATTTTCTTGTTTATAAAGGCTTAAATATGACAAGTGATGAAGTTGCAATTTATTGGTATTTGCATTTCGACTCTTAA", "fmax": "2933889", "accession": "AE016879.1", "fmin": "2933334", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacillus anthracis str. Ames", "NCBI_taxonomy_id": "198094", "NCBI_taxonomy_cvterm_id": "43244"}, "protein_sequence": {"accession": "AAP26981.1", "sequence": "MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNEELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHFDS"}}}}, "ARO_category": {"37249": {"category_aro_name": "streptothricin acetyltransferase (SAT)", "category_aro_cvterm_id": "37249", "category_aro_accession": "3000869", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine)."}, "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."}, "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."}}, "ARO_name": "SatA", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43243", "model_name": "SatA", "model_type_id": "40292"}, "3789": {"model_id": "3789", "ARO_accession": "3005036", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. BLMT confers resistance to bleomycin.", "model_sequences": {"sequence": {"6084": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGACCAAGCGACGCCCAACCTGCCATCACGAGATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGCTGGAGTTCTTCGCCCACCCCGGGCTCGATCCCCTCGCGAGTTGGTTCAGCTGCTGCCTGAGGCTGGACGACCTCGCGGAGTTCTACCGGCAGTGCAAATCCGTCGGCATCCAGGAAACCAGCAGCGGCTATCCGCGCATCCATGCCCCCGAACTGCAGGAGTGGGGAGGCACGATGGCCGCTTTGGTCGACCCGGACGGGACGCTCCTGCGCCTGATACAGAACGAATTGCTTGCAGGCATCTCATGA", "fmax": "117657", "accession": "AB255435.1", "fmin": "117276", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "BAF34030.1", "sequence": "MTDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNELLAGIS"}}}}, "ARO_category": {"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."}, "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."}, "41420": {"category_aro_name": "Bleomycin resistant protein", "category_aro_cvterm_id": "41420", "category_aro_accession": "3004256", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Bleomycin resistant proteins (BRP) confer resistance to bleomycin and to bleomycin-like molecules."}}, "ARO_name": "BLMT", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43234", "model_name": "BLMT", "model_type_id": "40292"}, "3808": {"model_id": "3808", "ARO_accession": "3005072", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-2 is a beta-lactamase from the blaROB AMR gene family. It was found in Bibersteinia trehalosi.", "model_sequences": {"sequence": {"6103": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCTCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "88218", "accession": "CP003745.1", "fmin": "87300", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bibersteinia trehalosi USDA-ARS-USMARC-192", "NCBI_taxonomy_id": "1171377", "NCBI_taxonomy_cvterm_id": "43277"}, "protein_sequence": {"accession": "AGH37381.1", "sequence": "MFNKLKIGTLLLLTLTACSLNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43276", "model_name": "ROB-2", "model_type_id": "40292"}, "3814": {"model_id": "3814", "ARO_accession": "3005079", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-9 is a class A beta-lactamase from the blaROB AMR gene family It is described by Kadlec et al.", "model_sequences": {"sequence": {"6111": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAAAGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAAAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "929", "accession": "MH316128.1", "fmin": "8", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mannheimia haemolytica", "NCBI_taxonomy_id": "75985", "NCBI_taxonomy_cvterm_id": "39540"}, "protein_sequence": {"accession": "AWU47610.1", "sequence": "MLNKLKIGTLLLLTLTACSPNSVHSVKSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-9", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43286", "model_name": "ROB-9", "model_type_id": "40292"}, "3756": {"model_id": "3756", "ARO_accession": "3005012", "model_param": {"blastp_bit_score": {"param_value": "775", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "blaIDC-1 is an IDC class C beta-lactamase and an integron cephalosprinase", "model_sequences": {"sequence": {"6046": {"dna_sequence": {"partial": "0", "sequence": "ATGCCGAGAACTGAATCCGTGCCATCCAAGTCCCTTGTTGTTAGGACGCTGCTGCTCGTCTTCGCCTGCCTCTTTCCTATGGCAGTTCCAGCAGTCGAAGACTCCTCCCGTGTCCGCGCCGCCGTCGACGCCGCGATCCTGCCCTTAATGTCCCAGCATGACATCCCCGGCATGGCTGTCGGGCTGATCCTCGATGGCCAGCCCTATGTTGTTACGTATGGCGTCGCCTCGAAGGAAACCAACGTACCCGTAGCGGAGGCAACACTATTCGAGATCGGCTCCGTCAGCAAAGTCTTCACCGCAACGCTGGCCACCTACGCGCAAGCCACCGGCAAATTGTCCCTGGACGACCATCCGGGCAAGTACCTGCCGCATTTAAAAGGCGCGCCGATCGACCAAGCCACGTTGCTTCACCTGGGAACCTACACCGCCGGCGGACTGCCGTTGCAGTTCCCTGATGAGGTGACGGGAGAGGCGGCGGTGATGAACTACTTCCGCAACTGGACGCCGCTGGCTCCCCCGGGCACACGGCGCGAGTACTCCAACGCAAGCCCGGGCTTGCTCGGGGTTGTTGCGGCCAGCGCGCTGGATGACGATTTCGCGACGTTGATGCAAACGACGGTATTTCCCGCATTCGGCATGACGGACAGCTTCATTCACGTGCCGGACCGCAAGATGCCGGACTACGCGTGGGGCTATCGCAAGGACAGACGGGTCCGTGTGAACGAGGGGCCGCTTGACGAGCAGGCTTACGGCGTCAAGACGACGGTGTCGGACTTGCTCCGCTTCGTGCAGGCGAACATCGATCCGAACTCGCTCGAGCCGTCGATGCGCCACGCCGTCGAAGCCACGCAGGTCGGATACTTCCGCGCGGGGACTCTGGTGCAGGGCCTTGGGTGGGAAAAGTATCCGTACCCTGTCTCACGCGAATGGCTGCTCGGCGGCAACGCCAAGGAGATGCTTTTCGATCCACAGCCTGCCTATCGGCTGACGGACCAGACCGCAGGCGGACAGTATCTCTTTAACAAGACGGGATCGACCGGCGGCTTCGCCACTTACGTGGCATTCGTGCCCGCTAGGAAGATCGGGATCGTCATGCTGGCAAACCGGAGTTATCCAATTCCGGATCGCGTTGAGGCCGCCTGGATGATCTTGGAACAACTTGCATCGGGGACCGACTCAAATTGA", "fmax": "1290", "accession": "MN985649.1", "fmin": "102", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "sediment metagenome", "NCBI_taxonomy_id": "749907", "NCBI_taxonomy_cvterm_id": "43201"}, "protein_sequence": {"accession": "QIB98918.1", "sequence": "MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDSSRVRAAVDAAILPLMSQHDIPGMAVGLILDGQPYVVTYGVASKETNVPVAEATLFEIGSVSKVFTATLATYAQATGKLSLDDHPGKYLPHLKGAPIDQATLLHLGTYTAGGLPLQFPDEVTGEAAVMNYFRNWTPLAPPGTRREYSNASPGLLGVVAASALDDDFATLMQTTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRRVRVNEGPLDEQAYGVKTTVSDLLRFVQANIDPNSLEPSMRHAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEMLFDPQPAYRLTDQTAGGQYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWMILEQLASGTDSN"}}}}, "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."}, "43199": {"category_aro_name": "IDC beta-lactamase", "category_aro_cvterm_id": "43199", "category_aro_accession": "3005011", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "IDC beta-lactamases are class C beta-lactamases inc. cephalosporinases and carbapenemases."}}, "ARO_name": "IDC-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43200", "model_name": "IDC-1", "model_type_id": "40292"}, "3810": {"model_id": "3810", "ARO_accession": "3005074", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-4 is a beta-lactamase from the blaROB AMR gene family. It was found in Moraxella porci.", "model_sequences": {"sequence": {"6105": {"dna_sequence": {"partial": "0", "sequence": "ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATACAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "1004", "accession": "MUYV01000026.1", "fmin": "80", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella porci DSM 25326", "NCBI_taxonomy_id": "573983", "NCBI_taxonomy_cvterm_id": "43280"}, "protein_sequence": {"accession": "OOS22656.1", "sequence": "MLNKLKIGTLLLLTLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDTAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43279", "model_name": "ROB-4", "model_type_id": "40292"}, "3809": {"model_id": "3809", "ARO_accession": "3005073", "model_param": {"blastp_bit_score": {"param_value": "620", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ROB-3 is a beta-lactamase from the blaROB AMR gene family. It was found in Moraxella pluranimalium.", "model_sequences": {"sequence": {"6104": {"dna_sequence": {"partial": "0", "sequence": "ATGTTGAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATACAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA", "fmax": "7821", "accession": "MUYU01000013.1", "fmin": "6897", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella pluranimalium", "NCBI_taxonomy_id": "470453", "NCBI_taxonomy_cvterm_id": "42209"}, "protein_sequence": {"accession": "OOS23853.1", "sequence": "MLNKLKIGTLLLLTLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"}}}}, "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, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. 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."}, "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."}, "39428": {"category_aro_name": "ROB beta-lactamase", "category_aro_cvterm_id": "39428", "category_aro_accession": "3002994", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ROB beta-lactamases are a class A beta-lactamases."}}, "ARO_name": "ROB-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43278", "model_name": "ROB-3", "model_type_id": "40292"}, "3763": {"model_id": "3763", "ARO_accession": "3005021", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cfr(D) is found in Enterococcus faecium. It confers resistance to vancomycin, teicoplanin, and linezolid.", "model_sequences": {"sequence": {"6053": {"dna_sequence": {"partial": "0", "sequence": "ATGTTACAAAAACAATTAACTAAATATCAACAAATTGAAAAAGTTTTAAAAGAGTGTCAACAACCAAACTACCGAATGAAGCAAATTCTTCATTGTATTTTTAAAGAGAAAAAAACAGATTTCAATGAGATGTCTGTATTACCTAAAAATTTACGAGATACTTTAACAACAGAAATAGGAACATCACTTCTAACAGTTGAGCCCCTTATTGAACAGAAGTCGCAACAAGTGAGGAAAGTACTCTTTAATCTTTCTGGAGATAATCGCATTGAAACAGTCAACATGACCTATCAAGCTGGCTGGGAATCTTTTTGTATTTCATCTCAATGTGGCTGCAATCTAGGTTGTCAATTTTGCGCTACTGGAAAAATTGGCTTAAGAAAAAATTTAACGGCTGAGGAAATAACGGATCAAGTTCTCTACTTTCTTTTAAAAGGACACCAAATTGATAGTATTTCTTTTATGGGTATGGGAGAACCACTTGCTAACCCTCATTTTTTTGAGGCTTTAGATATTTTTATGAATCCTGATATGTTTCAACTGAGCCCTAGGCGTTTATCTGTTTCAACGATTGGTGTGATTCCTAAAATAAAACGACTAACAGCTGAATATCCACAAGTTCATTTAACTTTTTCTCTTCACTCACCTTTTGATGAAGAGAGAAGTCAGTTAATGCCGATTAATAAAAGTTTTCCCCTTTTAAAAGTGATGGATACTTTAGATGAACATATAAAAGTAACTTCAAAAAAAGTTTACATTGCTTATATTTTACTACCTGATGTGAACGATTCTTTGACTCATGCAGTTGCTTTAGCAGATTTACTTCGCTCTCGGTATAAAAAAGGAAAGCTGTATCATGTCAATCTCATCAGGTACAATCCTACTTTTGATGCACCAAGAACGTTCAAGCAAGTAGATGAAAAGCAAGTTAAACTGTTCTATCAAACCTTAATATCTAAAGGCATAAATGTCACTATTAGAAGTCAGTTTGGAATTGAAATTGATGCTGCCTGTGGCCAATTATATGGAAATTATGAGATTAAAAACAAAAAAACAATCCAAGTAAATGACTAG", "fmax": "1074", "accession": "MG707078.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterococcus faecium", "NCBI_taxonomy_id": "1352", "NCBI_taxonomy_cvterm_id": "36779"}, "protein_sequence": {"accession": "AXY65402.1", "sequence": "MLQKQLTKYQQIEKVLKECQQPNYRMKQILHCIFKEKKTDFNEMSVLPKNLRDTLTTEIGTSLLTVEPLIEQKSQQVRKVLFNLSGDNRIETVNMTYQAGWESFCISSQCGCNLGCQFCATGKIGLRKNLTAEEITDQVLYFLLKGHQIDSISFMGMGEPLANPHFFEALDIFMNPDMFQLSPRRLSVSTIGVIPKIKRLTAEYPQVHLTFSLHSPFDEERSQLMPINKSFPLLKVMDTLDEHIKVTSKKVYIAYILLPDVNDSLTHAVALADLLRSRYKKGKLYHVNLIRYNPTFDAPRTFKQVDEKQVKLFYQTLISKGINVTIRSQFGIEIDAACGQLYGNYEIKNKKTIQVND"}}}}, "ARO_category": {"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."}, "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."}, "36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}, "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."}, "36341": {"category_aro_name": "Cfr 23S ribosomal RNA methyltransferase", "category_aro_cvterm_id": "36341", "category_aro_accession": "3000202", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin."}, "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": "cfr(D)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43212", "model_name": "cfr(D)", "model_type_id": "40292"}, "3807": {"model_id": "3807", "ARO_accession": "3005069", "model_param": {"blastp_bit_score": {"param_value": "100", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "rsmA is a gene that regulates virulence of Pseudomonas aeruginosa. However, its negative effect on MexEF-OprN overexpression has been noted to confer resistance to various antibiotics. It's Escherichia coli homolog is csrA.", "model_sequences": {"sequence": {"6102": {"dna_sequence": {"partial": "0", "sequence": "ATGCTGATTCTGACTCGTCGGGTCGGAGAGACCCTGATGGTAGGTGACGACGTCACCGTGACGGTACTGGGTGTCAAAGGGAACCAGGTGCGCATCGGCGTCAACGCGCCGAAGGAAGTCGCCGTACACCGGGAGGAAATTTACCAGCGCATCCAGAAAGAGAAAGATCAAGAGCCAAACCATTAA", "fmax": "1020", "accession": "AF061757.1", "fmin": "834", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AAC16242.1", "sequence": "MLILTRRVGETLMVGDDVTVTVLGVKGNQVRIGVNAPKEVAVHREEIYQRIQKEKDQEPNH"}}}}, "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."}, "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."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}, "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."}, "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."}, "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."}, "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."}, "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."}, "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."}}, "ARO_name": "rsmA", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43273", "model_name": "rsmA", "model_type_id": "40292"}}}