diff --git a/q2_amr/card/partition.py b/q2_amr/card/partition.py index 894c572..afed9cb 100644 --- a/q2_amr/card/partition.py +++ b/q2_amr/card/partition.py @@ -9,9 +9,100 @@ CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDGeneAnnotationDirectoryFormat, + CARDMAGsKmerAnalysisDirectoryFormat, + CARDReadsAlleleKmerAnalysisDirectoryFormat, + CARDReadsGeneKmerAnalysisDirectoryFormat, ) +def collate_mags_annotations( + annotations: CARDAnnotationDirectoryFormat, +) -> CARDAnnotationDirectoryFormat: + return _collate(annotations) + + +def collate_reads_allele_annotations( + annotations: CARDAlleleAnnotationDirectoryFormat, +) -> CARDAlleleAnnotationDirectoryFormat: + return _collate(annotations) + + +def collate_reads_gene_annotations( + annotations: CARDGeneAnnotationDirectoryFormat, +) -> CARDGeneAnnotationDirectoryFormat: + return _collate(annotations) + + +def collate_mags_kmer_analyses( + kmer_analyses: CARDMAGsKmerAnalysisDirectoryFormat, +) -> CARDMAGsKmerAnalysisDirectoryFormat: + return _collate(kmer_analyses) + + +def collate_reads_allele_kmer_analyses( + kmer_analyses: CARDReadsAlleleKmerAnalysisDirectoryFormat, +) -> CARDReadsAlleleKmerAnalysisDirectoryFormat: + return _collate(kmer_analyses) + + +def collate_reads_gene_kmer_analyses( + kmer_analyses: CARDReadsGeneKmerAnalysisDirectoryFormat, +) -> CARDReadsGeneKmerAnalysisDirectoryFormat: + return _collate(kmer_analyses) + + +def _collate(partition_list): + collated_partitions = type(partition_list[0])() + # For every partition + for partition in partition_list: + # For every sample + for sample in partition.path.iterdir(): + # If artifacts are annotations or kmer analyses from MAGs + if isinstance( + partition_list[0], + (CARDAnnotationDirectoryFormat, CARDMAGsKmerAnalysisDirectoryFormat), + ): + # For every MAG + for mag in sample.iterdir(): + # Create directories in collate. If dir already exists raise error + try: + os.makedirs(collated_partitions.path / sample.name / mag.name) + except FileExistsError as e: + raise FileExistsError( + f"The directory already exists: {e.filename}. MAG IDs must" + f" be unique across all artifacts. Each artifact in the" + f" list must be unique and cannot be repeated." + ) + + # Copy every file in the MAG directory to the collated directory + for file in mag.iterdir(): + duplicate( + file, + collated_partitions.path + / sample.name + / mag.name + / file.name, + ) + + # If artifacts are annotations or kmer analyses are from reads + else: + # Create directories in collate. If dir already exists raise error + try: + os.makedirs(collated_partitions.path / sample.name) + except FileExistsError as e: + raise FileExistsError( + f"The directory already exists: {e.filename}. Sample IDs must" + f" be unique across all artifacts. Each artifact in the" + f" list must be unique and cannot be repeated." + ) + + # Copy every file in the sample directory to the collated directory + for file in sample.iterdir(): + duplicate(file, collated_partitions.path / sample.name / file.name) + + return collated_partitions + + def partition_mags_annotations( annotations: CARDAnnotationDirectoryFormat, num_partitions: int = None ) -> CARDAnnotationDirectoryFormat: diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json new file mode 100644 index 0000000..d49ca4d --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json @@ -0,0 +1 @@ +{"k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588": {"gnl|BL_ORD_ID|1672|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanO cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1699", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002954", "ARO_name": "vanX gene in vanO cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 5.8564e-116, "bit_score": 326.635, "max_identities": 152, "cvterm_id": "36897", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "M DFV+VD+ VPGVRWDAKYAT DNFTGKPV+GYLANRIVGTRALC+ALE R++AAS GFGLLLWDGYRP+RAVDSFL W++QPEDG TK+RHYPNI R EM E+GYVA++SGHSRG VDLTLY L TG+L PMGG HDLMD ISHH A GI E+ NR LRS+ME CGF YD EWWHYTLK EPYPD YFDFP+T", "sequence_from_db": "MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT", "sequence_from_broadstreet": "MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT", "dna_sequence_from_broadstreet": "ATGAACGACGACTTCGTCTACGTCGACGACTGGGTGCCCGGAGTCCGCTGGGATGCCAAGTACGCCACGTGGGACAACTTCACCGGCAAACCGGTAGACGGCTACCTCGCGAATCGAATCGTCGGCACCCGGGCTTTGTGCGCGGCCCTCGAGCAAGCACGCGAGAAGGCAGCTTCCCTCGGCTTCGGATTGCTTCTCTGGGACGGCTACCGTCCTCGACGCGCCGTCGACAGCTTCCTACGCTGGTCAGAACAGCCGGAGGATGGCCAGACGAAGCAGCGACACTATCCCAATATCGACAGACCCGAGATGCTCGAAAAGGGATACGTGGCAACCCAGTCGGGCCACAGTAGGGGCGGCGCCGTTGACCTGACGCTCTATCACCTTGCGACCGGTGAACTTGCTCCTATGGGTGGCGACCACGACCTCATGGACCCGATCTCACATCATCGAGCGCGAGGAATCAAGCCAATCGAGTCCAAGAATCGTGAGCTTCTTCGTTCCATCATGGAGGACTGCGGATTTGATCGGTACGACTGCGAGTGGTGGCACTACACGCTGAAACGCGAACCATATCCAGATGTCTACTTCGACTTTCCGATCACGTGA", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 75.25}, "gnl|BL_ORD_ID|2066|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanI cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "2243", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3003725", "ARO_name": "vanX gene in vanI cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.67433e-112, "bit_score": 317.39, "max_identities": 147, "cvterm_id": "42687", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "MK DFVFVDE V G+RWDAKYAT DNFTGKPV+GY ANRIVGTRALC+ALE R+ AAS GFGLLLWDGYRPQ AVD FL W+KQPEDG TK++HYPNI R+E+ E+GYVA+KSGHSRGS +DLTLY L +G LVPMGG DLMD +SHHGA GI++AE NR L S+MEA GF SY EWWHY+LK+EPYP+TYFDF + ", "sequence_from_db": "MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA", "sequence_from_broadstreet": "MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA", "dna_sequence_from_broadstreet": "ATGAAAAGTGATTTTGTCTTTGTGGACGAGTTGGTATCAGGAATACGTTGGGATGCTAAATACGCCACCTGGGATAATTTTACCGGCAAACCGGTGGACGGCTATGCAGCCAATCGAATTGTCGGTACGAGAGCGTTGTGCGCGGCCTTGGAAAAAGCACGGGAAAACGCCGCATCCTTGGGCTTTGGCTTGCTTCTTTGGGATGGTTACCGCCCTCAATGCGCCGTAGATTGCTTTCTGCGCTGGTCTAAACAGCCGGAAGATGGCCGGACGAAACAGAAACACTATCCGAATATTGACCGATCCGAGATCATCGAAAAAGGATATGTGGCTGCCAAGTCGGGCCACAGCCGGGGCAGCGCCATTGATTTAACCCTTTATCATTTAGCTTCCGGAACACTTGTGCCCATGGGCGGTGATTTTGATTTGATGGATTCAGTCTCACATCATGGCGCACATGGAATCAGCCAAGCCGAAGCGAGAAACCGTCAATATCTTTGTTCGATCATGGAGGCCAGCGGTTTTGTTTCCTACGCTTGCGAGTGGTGGCATTACAGCCTGAAACACGAACCTTATCCCAACACTTACTTTGATTTTCTCATCGCCTAG", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 72.77}, "gnl|BL_ORD_ID|1499|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanF cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1509", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002952", "ARO_name": "vanX gene in vanF cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.33452e-99, "bit_score": 286.189, "max_identities": 134, "cvterm_id": "39542", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ DFVF+DE + GVRWD+KYAT DNFTGKPV+GY NRI GT AL AL V+++AA+ G+GLLLWDGYRPQRAV+ FLHW+ QPEDG TK R+YPNI R EM +GYVASKS HSRGS +DLTLY L TG LVPMG G D MDE SHH + GI+ E NR L S+ME GF SY EWWHY L+NEPYP +YFDFP+", "sequence_from_db": "MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPI", "sequence_from_broadstreet": "MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPIGGNHLDPFSNFCGTVPLDALSP", "dna_sequence_from_broadstreet": "ATGGAAAAAGATTTTGTTTTTTTAGATGAAATATTGCATGGAGTTCGTTGGGACTCCAAATATGCCACATGGGACAATTTCACTGGAAAACCGGTAGACGGATATGAAGTCAATCGCATAGCGGGGACATATGCTTTGGCTGTTGCGCTGCTGGAGGTAAAGAAGCAGGCGGCTGCTCTAGGGTACGGCTTGCTCCTGTGGGATGGCTATCGTCCTCAACGTGCGGTAAACTGTTTCTTGCATTGGTCTGCGCAGCCGGAAGACGGCCGCACAAAAGAAAGATATTATCCCAATATTGATCGGATCGAGATGGTTACAAAGGGATATGTGGCTTCAAAATCAAGCCACAGTCGCGGAAGCGCGATTGACCTTACGCTTTATCGATTGGACACGGGTGCGCTTGTCCCTATGGGGAGCGGCTTCGATTTTATGGATGAACGTTCACATCATACCTCAAAAGGAATTTCAAGTAACGAAGCGCAAAATCGCCAGTTATTATGTTCTATTATGGAATACAGCGGATTTGAATCATATGTATATGAATGGTGGCACTACGTATTAAGAAACGAACCATACCCCAGCAGCTATTTTGATTTTCCCATTGGCGGGAACCATCTAGACCCATTTTCCAACTTTTGTGGGACAGTGCCACTTGATGCGTTGTCGCCCTAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 66.67}, "gnl|BL_ORD_ID|4672|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanA cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "217", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002949", "ARO_name": "vanX gene in vanA cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.30871e-95, "bit_score": 274.633, "max_identities": 127, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ F F+DE V GVRWDAKYAT DNFTGKPV+GY NRIVGT L +L ++ AA++G+GLLLWDGYRP+RAV+ F+ WA QPE+ TK +YPNI R EM +GYVASKS HSRGS +DLTLY L TG+LVPMG D MDE SHH A GI+ E NR LRS+ME GF +Y EWWHY L++EPYP++YFDFPV", "sequence_from_db": "MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPV", "sequence_from_broadstreet": "MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK", "dna_sequence_from_broadstreet": "ATGGAAATAGGATTTACTTTTTTAGATGAAATAGTACACGGTGTTCGTTGGGACGCTAAATATGCCACTTGGGATAATTTCACCGGAAAACCGGTTGACGGTTATGAAGTAAATCGCATTGTAGGGACATACGAGTTGGCTGAATCGCTTTTGAAGGCAAAAGAACTGGCTGCTACCCAAGGGTACGGATTGCTTCTATGGGACGGTTACCGTCCTAAGCGTGCTGTAAACTGTTTTATGCAATGGGCTGCACAGCCGGAAAATAACCTGACAAAGGAAAGTTATTATCCCAATATTGACCGAACTGAGATGATTTCAAAAGGATACGTGGCTTCAAAATCAAGCCATAGCCGCGGCAGTGCCATTGATCTTACGCTTTATCGATTAGACACGGGTGAGCTTGTACCAATGGGGAGCCGATTTGATTTTATGGATGAACGCTCTCATCATGCGGCAAATGGAATATCATGCAATGAAGCGCAAAATCGCAGACGTTTGCGCTCCATCATGGAAAACAGTGGGTTTGAAGCATATAGCCTCGAATGGTGGCACTATGTATTAAGAGACGAACCATACCCCAATAGCTATTTTGATTTCCCCGTTAAATAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.18}, "gnl|BL_ORD_ID|1647|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanB cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1666", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002950", "ARO_name": "vanX gene in vanB cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.96956e-95, "bit_score": 274.248, "max_identities": 128, "cvterm_id": "35918", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "M+ F+F+DE + GVRWDAKYAT DNFTGKPV+GY NRI+GT+A+ AL + AA G+GLLLWDGYRP+ AVD FL WA QPED TK ++YPNI RAE+ +GYVAS+S HSRGST+DLTLY L TG+LV MG D MDE SHH A GI AE NR LR +ME+ GF SY EWWHY L +EPYPDTYF+F V+", "sequence_from_db": "MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS", "sequence_from_broadstreet": "MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS", "dna_sequence_from_broadstreet": "ATGGAAAATGGTTTTTTGTTTTTAGATGAAATGTTGCATGGTGTTCGTTGGGATGCCAAGTACGCTACATGGGATAACTTCACGGGAAAACCAGTGGATGGGTATGAGGTGAATCGCATCATCGGCACAAAGGCCGTGGCGCTTGCTCTGCGCGAAGCACAAATCCATGCGGCACGCCTTGGCTACGGCTTGCTTTTATGGGATGGATATCGGCCAAAATCTGCGGTGGACTGTTTCCTGCGTTGGGCGGCGCAGCCGGAGGACAACCTCACAAAAGAAAAATATTACCCCAATATTGAGCGAGCCGAGTTGATTACAAAGGGCTATGTGGCCTCACAATCCAGCCATAGCCGTGGAAGCACAATTGATCTTACGCTCTACCACTTGGATACAGGGGAACTTGTTTCAATGGGAAGCAACTTCGATTTTATGGACGAACGGTCGCACCATACAGCAAAAGGGATAGGGAATGCAGAGGCACAAAATCGAAGATGCTTGCGTAAAATCATGGAAAGCAGCGGATTTCAGTCCTATCGCTTTGAATGGTGGCACTATAAGTTGATTGATGAGCCATACCCCGATACCTATTTTAATTTTGCTGTTTCATAA", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.37}, "gnl|BL_ORD_ID|1502|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanD cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1566", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3003070", "ARO_name": "vanX gene in vanD cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 3.44626e-94, "bit_score": 271.552, "max_identities": 125, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ +FVF+DE +PG+RWDAKYAT DNFTGKPV+GY NRIVGT+ L +AL ++ A G+GLLLWDGYRPQ AVD FL WA PE+ TK+R+YPNI R EM +GYVAS+S HSRGS +DLT++ L TG LVPMGG D MD SHH A G++ E GNR LR +ME GF +Y EWWHY L +EPYPDTYFDF +", "sequence_from_db": "MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCI", "sequence_from_broadstreet": "MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCIA", "dna_sequence_from_broadstreet": "ATGGAAAAGAACTTTGTCTTTTTGGATGAAATGCTGCCGGGCATCCGGTGGGATGCCAAATATGCCACATGGGACAATTTCACCGGGAAACCGGTAGACGGATACGAGGTAAACCGCATTGTGGGAACGAAAGAGCTTGGTGCCGCTTTACGTAAGGCACAGAAGGCGGCGGAGAAACTGGGATACGGTCTGCTCTTATGGGACGGCTACCGTCCCCAGTGTGCAGTGGACTGCTTTTTGACTTGGGCTTCCCTGCCGGAGAACAATCTGACGAAAAAGCGTTACTACCCAAATATCAAAAGGAACGAGATGATCACGAAAGGGTATGTGGCTTCTCAGTCCAGCCACAGTCGCGGGAGCGCGATTGATCTCACGATTTTTCGTTTGGACACGGGTATGCTTGTGCCAATGGGCGGAGATTTCGACTTTATGGATGTACGGTCGCATCATGCCGCCAGTGGTCTGAGCGAAGAGGAGGCCGGAAACCGTGAGCGCCTGCGTGATATCATGGAGCGCAGCGGATTTGAAGCCTACCGATATGAATGGTGGCATTATGTCTTGGCAGACGAGCCATACCCGGATACATATTTTGATTTTTGCATTGCCTAG", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 62.19}, "gnl|BL_ORD_ID|4822|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanP cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "5806", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3007190", "ARO_name": "vanX gene in vanP cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 5.82743e-94, "bit_score": 271.166, "max_identities": 121, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "MK +FV++DE +PGVRWDAKYAT DNF G PV GY NR+VGT + AL+ V + A +G GLLLWDGYRP RAV F+ W K+ +D + K +HYP+I + M E GY+A SGHSRGST+DLTLYDL + L+ MGG DLMDEISH+ A GIT+ E NR LR LM CGF Y++EWWHY+LK+EPYPDTYFDF +", "sequence_from_db": "MKSEFVYLDEVIPGVRWDAKYATWDNFMGMPVNGYQVNRVVGTVEMADALKEVSKLAKEKGVGLLLWDGYRPVRAVSHFMEWVKKSKDESRKAKHYPHIDKKTMIEEGYIAEYSGHSRGSTIDLTLYDLESKKLLDMGGDFDLMDEISHYAAEGITKEEKENRKLLRDLMVKCGFVPYENEWWHYSLKDEPYPDTYFDFVI", "sequence_from_broadstreet": "MKSEFVYLDEVIPGVRWDAKYATWDNFMGMPVNGYQVNRVVGTVEMADALKEVSKLAKEKGVGLLLWDGYRPVRAVSHFMEWVKKSKDESRKAKHYPHIDKKTMIEEGYIAEYSGHSRGSTIDLTLYDLESKKLLDMGGDFDLMDEISHYAAEGITKEEKENRKLLRDLMVKCGFVPYENEWWHYSLKDEPYPDTYFDFVIE", "dna_sequence_from_broadstreet": "ATGAAATCAGAATTTGTTTATTTGGATGAAGTAATACCGGGAGTAAGATGGGATGCAAAATATGCTACTTGGGATAATTTTATGGGAATGCCTGTTAATGGTTATCAGGTCAATCGTGTTGTAGGTACAGTTGAGATGGCAGATGCCTTAAAGGAGGTCAGTAAGCTTGCAAAGGAAAAGGGCGTTGGTTTACTTTTGTGGGATGGATACCGTCCTGTCCGTGCGGTTTCCCACTTTATGGAATGGGTAAAAAAGAGTAAAGATGAAAGCCGTAAGGCGAAGCATTATCCACATATTGATAAAAAGACGATGATAGAGGAAGGCTACATTGCAGAGTATTCCGGTCACAGCAGGGGAAGTACGATTGATTTGACACTGTATGATTTGGAAAGCAAAAAGCTTCTGGACATGGGTGGGGATTTTGATTTGATGGACGAAATCTCCCACTATGCGGCAGAGGGGATTACCAAGGAAGAGAAGGAGAATCGTAAATTACTTCGGGATTTGATGGTCAAATGCGGATTTGTTCCATATGAAAATGAATGGTGGCATTATTCGTTAAAAGACGAGCCATATCCGGATACATATTTTGACTTTGTCATTGAATAG", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 60.2}, "gnl|BL_ORD_ID|1951|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanM cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1996", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002953", "ARO_name": "vanX gene in vanM cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 7.41369e-94, "bit_score": 270.781, "max_identities": 127, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ F F+DE + VRWDAKYAT DNFTGKP++GY NRI+GT L AL V++ A ++G+GLLLWDGYRPQ+AV+ FL WA QPED TK ++YPNI R EM +GYVASKS HSRGS +DLTLY L T +LVPMG G D MDE SHH A GIT E NR LRS+ME GF +Y EWWHY L NEPYP + FDFPV", "sequence_from_db": "MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPV", "sequence_from_broadstreet": "MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPVK", "dna_sequence_from_broadstreet": "ATGGAAAAAGGATTTACCTTTTTAGATGAAATATTAAACGATGTTCGTTGGGACGCTAAATATGCTACGTGGGACAACTTCACTGGAAAACCAATTGATGGATATGAAGTAAATCGAATTATAGGAACATATGAGTTAGCCGATGCGCTATTGAAGGTTCAAGAATTAGCTTTTAACCAAGGTTATGGATTGCTTTTATGGGACGGTTACCGTCCCCAACAAGCTGTAAATTGTTTTTTGCAATGGGCGGCACAGCCGGAAGATAATCGAACAAAGGCAAAATATTATCCCAATATTGACCGAACTGAGATGGTTTCAAAAGGATACGTGGCTTCAAAATCAAGTCATAGCCGCGGAAGTGCAATTGATCTTACACTTTATCGATTAGACACGGACGAACTTGTTCCGATGGGGAGCGGATTTGATTTTATGGATGAGCGCTCTCATCATGAGGCAAAAGGAATTACGAGCAATGAAGCGCAAAACCGTAGATTTTTGCGTTCCATTATGGAAAACAGTGGGTTTGAAGCGTATAGTTTCGAATGGTGGCACTATGTATTGATAAACGAACCTTATCCCTATAGCTGCTTTGATTTTCCTGTCAAATAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.18}}, "k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658": {"gnl|BL_ORD_ID|1673|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanM cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1713", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002961", "ARO_name": "vanY gene in vanM cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 4.74333e-24, "bit_score": 90.8929, "max_identities": 56, "cvterm_id": "36779", "query": "EAAGAYRQMAAEAGAAGVP-MSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGL", "match": "+ A + +M A GV S SGFR EQ+ LY ++ A GYSEH GLA+DI G+ +E +E G W NA YGFI+RYP ITG +EPWH RYVG H+ + + LEEYL ", "sequence_from_db": "KVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPA--------GYSEHNLGLALDI----GSTQME--MSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDF", "sequence_from_broadstreet": "MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR", "dna_sequence_from_broadstreet": "ATGGTCTTTCAAGGAAACTTACTCTTGGTTAATAACGAATATCCGGTTCTCGAAGAGAGTATAAAAACAGACGTTGTAAATTTATTTAAACATGATGAATTGACAAAAGGATATGAATTGCTCAATAGGGAAATTTATTTATCGGAGAAAGTTGCCCGTGAATTTTCAGAGATGGTAGATGCGGCTGAAAAAGAAGGAGTTCGCCATTTTTCAATCAATAGTGGGTTTCGAAACTTTGATGAGCAAAATGCCCTTTATCAAGAAATGGGGTCTGACTACGCCTTGCCTGCAGGTTATAGCGAACATAATTTAGGTTTAGCACTTGATATCGGATCTACTCAAATGGAAATGAGTGAGGCACCGGAAGGAAAGTGGCTAGAAGATAATGCGTGGGAATACGGCTTTATTTTACGCTATCCAATGGACAAAACGGCCATCACAGGTATTCAGTATGAACCTTGGCATTTTCGCTATGTGGGATTACCGCACAGTGCAATTATAGAGGAAAAGAATTTTGCTTTAGAAGAATATTTGGATTTCCTAAAAGAACAAAAATCCATTTCAGGTACTATACATGGCGAAAATTATGAGATTTCTTATTATCCTATTACCGAAAAAACAGACATTGAAATGCCTGCCAATCTTCATTATGAAATATCAGGAAACAATATGGATGGTGTGATTGTGACAGTGTATCGCTAA", "partial": "0", "query_start": 1, "query_end": 432, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 38.62}, "gnl|BL_ORD_ID|1808|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanF cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1899", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002958", "ARO_name": "vanY gene in vanF cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.41093e-23, "bit_score": 90.8929, "max_identities": 53, "cvterm_id": "39542", "query": "EAAGAYRQMAAEAGAAGVPMSAVS-GFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "E AG + +M A A GV +S G+R EQ +LY +F A G+SEH GL++D+ G+ ++ A G W N YGFI+RYP +TG +EPWH+RYVG H+ M + LEEYL", "sequence_from_db": "EIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPA--------GHSEHNLGLSLDV----GSTQMKMDKAP--EGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYL", "sequence_from_broadstreet": "MKKWGLLLVFALFLVFIFNILPISQDKVEDRIYEQNDKDTSDDKMTAENMQKIELTEEQIYQGNLLLVNNEHPVHQKSIKSDIINLFTHKELTKGYGLLDNEIKLSEEIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPAGHSEHNLGLSLDVGSTQMKMDKAPEGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYLDYLKEEKSISVRVDGKKYTISYDPISQNETIEVEVPADEQYEISGNNIDGVIVTTFS", "dna_sequence_from_broadstreet": "ATGAAAAAGTGGGGACTTTTATTGGTTTTTGCATTATTTCTAGTATTTATTTTTAATATATTACCGATATCCCAAGATAAAGTAGAGGATCGAATATATGAACAAAATGACAAAGATACATCGGATGATAAAATGACAGCTGAAAATATGCAAAAGATTGAGCTTACGGAAGAGCAGATCTATCAAGGGAATCTACTCTTGGTCAACAATGAACATCCTGTTCACCAAAAGAGTATAAAATCGGATATTATAAATTTATTTACGCACAAAGAATTGACAAAGGGGTATGGGTTACTTGATAACGAAATTAAATTGTCAGAGGAAATAGCTGGGAAATTTTCAGAGATGATAGCTGCGGCTGAAGAGGATGGCGTTAGTAATTTTTTAATTAGCAGTGGTTATCGAGACTTGGATGAGCAAAGCAGACTTTATGAGGAAATGGGTTCTGATTTTGCTTTGCCAGCAGGTCATAGTGAACACAACTTGGGGTTATCGCTTGATGTAGGATCTACTCAAATGAAGATGGATAAAGCGCCTGAAGGAAAGTGGATAGAAAAAAATTGTTGGGAATACGGCTTTATATTACGCTATCCCTTGGATAAAACGGATGTTACAGGAATTCAATATGAACCTTGGCATATTCGCTATGTCGGTTTGCCTCACAGTGCGATTATGCAGGAAATGAATTTAGCTTTGGAAGAATATTTAGATTATTTAAAAGAAGAAAAGAGCATTTCTGTTCGTGTTGATGGGAAAAAATATACAATTTCATATGATCCCATTTCTCAAAACGAGACAATTGAAGTTGAAGTACCAGCGGATGAACAGTATGAAATATCTGGTAATAATATTGATGGAGTAATTGTGACCACATTTTCTTGA", "partial": "0", "query_start": 1, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 37.06}, "gnl|BL_ORD_ID|4732|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanG cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "298", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002959", "ARO_name": "vanY gene in vanG cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 6.26485e-23, "bit_score": 88.5817, "max_identities": 56, "cvterm_id": "35918", "query": "AAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPE---------AADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "A E +PM VSG+RT +Q LY F E A+ A PG+SEHQ G A+DI L W N+ YGFI RYP ITG A E WH RYVG E A M++ G LEEYL", "sequence_from_db": "AREENWGELPM-VVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYL-----------WLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYL", "sequence_from_broadstreet": "MNHMNMKHRRRKRRRNQSFLFTGILLLVVVSASSFLWYGFGNAAKKDSVIEEMPFTITQDGMQAKEEIKKTVLETSYGGKQQVAEENHGNTQNAGTDEAWNLMLVNRDNAIPDNYEVNLVEVEGGERVDERIYEPLMEMLNAAREENWGELPMVVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYLWLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYLEKKQSEN", "dna_sequence_from_broadstreet": "ATGAACCATATGAATATGAAACACAGACGCAGAAAACGCAGACGTAACCAATCTTTTTTGTTCACAGGAATTTTACTCTTAGTTGTAGTATCTGCAAGCAGTTTTTTATGGTACGGTTTTGGCAATGCGGCAAAAAAAGACAGTGTTATTGAAGAAATGCCATTTACCATTACACAGGACGGAATGCAGGCAAAGGAAGAAATAAAGAAAACGGTACTGGAAACTTCCTATGGCGGCAAACAGCAGGTAGCGGAAGAAAATCACGGCAATACACAAAATGCAGGGACAGACGAAGCGTGGAATTTAATGCTTGTCAACAGAGATAATGCGATTCCAGACAATTACGAAGTAAATCTGGTCGAAGTAGAGGGCGGGGAGCGTGTAGATGAGCGTATCTATGAACCTCTTATGGAAATGCTTAATGCGGCAAGGGAGGAAAACTGGGGCGAATTGCCGATGGTAGTATCTGGCTATCGGACGCAGGAAAAACAGCAGAGCCTTTATGATGAAAAGATTGCAAAGTTCAAAAAAGAGGGGTATTCAGACAGTGAAGCCGTAAGGCAGGCAGAACAATGGGTTGCAGTGCCAGGTCACAGTGAGCATCAGCTCGGTTTTGCAGTGGATATTAACGGGGCAACTTATGATGTTTATCTATGGTTGCAGGAAAACAGCTATAAATACGGCTTTATCTTCAGATATCCCGGCAGTAAAACGGATATTACCGGGACTGCTGAAGAAGTATGGCATTACCGTTATGTTGGAGTGGAAGCGGCAACTGAAATGTATGAAAATGGATTATGTCTTGAGGAATATCTTGAGAAAAAGCAATCAGAAAACTAA", "partial": "0", "query_start": 28, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 39.44}, "gnl|BL_ORD_ID|4669|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanA cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "89", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002955", "ARO_name": "vanY gene in vanA cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 3.428e-22, "bit_score": 87.0409, "max_identities": 52, "cvterm_id": "36779", "query": "EAAGAYRQMAAEAGAAGVPMSAV-SGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "E A + +M +A GV + SG+R EQ LY + G E A GYSEH +GL++D+ + +E G W NA YGFI+RYP +TG +EPWH+RYVG H+ M + LEEY+", "sequence_from_db": "EIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLY----QEMGAEYA----LPAGYSEHNSGLSLDVGS--SLTKMERA----PEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYM", "sequence_from_broadstreet": "MKKLFFLLLLLFLIYLGYDYVNEALFSQEKVEFQNYDQNPKEHLENSGTSENTQEKTITEEQVYQGNLLLINSKYPVRQESVKSDIVNLSKHDELINGYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLYQEMGAEYALPAGYSEHNSGLSLDVGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYMDYLKEEKTISVSVNGEKYEIFYYPVTKNTTIHVPTNLRYEISGNNIDGVIVTVFPGSTHTNSRR", "dna_sequence_from_broadstreet": "ATGAAGAAGTTGTTTTTTTTATTGTTATTGTTATTCTTAATATACTTAGGTTATGACTACGTTAATGAAGCACTGTTTTCTCAGGAAAAAGTCGAATTTCAAAATTATGATCAAAATCCCAAAGAACATTTAGAAAATAGTGGGACTTCTGAAAATACCCAAGAGAAAACAATTACAGAAGAACAGGTTTATCAAGGAAATCTGCTATTAATCAATAGTAAATATCCTGTTCGCCAAGAAAGTGTGAAGTCAGATATCGTGAATTTATCTAAACATGACGAATTAATAAATGGATACGGGTTGCTTGATAGTAATATTTATATGTCAAAAGAAATAGCACAAAAATTTTCAGAGATGGTCAATGATGCTGTAAAGGGTGGCGTTAGTCATTTTATTATTAATAGTGGCTATCGAGACTTTGATGAGCAAAGTGTGCTTTACCAAGAAATGGGGGCTGAGTATGCCTTACCAGCAGGTTATAGTGAGCATAATTCAGGTTTATCACTAGATGTAGGATCAAGCTTGACGAAAATGGAACGAGCCCCTGAAGGAAAGTGGATAGAAGAAAATGCTTGGAAATACGGGTTCATTTTACGTTATCCAGAGGACAAAACAGAGTTAACAGGAATTCAATATGAACCATGGCATATTCGCTATGTTGGTTTACCACATAGTGCGATTATGAAAGAAAAGAATTTCGTTCTCGAGGAATATATGGATTACCTAAAAGAAGAAAAAACCATTTCTGTTAGTGTAAATGGGGAAAAATATGAGATCTTTTATTATCCTGTTACTAAAAATACCACCATTCATGTGCCGACTAATCTTCGTTATGAGATATCAGGAAACAATATAGACGGTGTAATTGTGACAGTGTTTCCCGGATCAACACATACTAATTCAAGGAGGTAA", "partial": "0", "query_start": 1, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 36.36}, "gnl|BL_ORD_ID|602|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanB cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "556", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002956", "ARO_name": "vanY gene in vanB cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.3754e-20, "bit_score": 82.4185, "max_identities": 56, "cvterm_id": "35918", "query": "AGAAGVPMSAVSGFRTGAEQDQLY---------VSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLG", "match": "A A GV SG+RT +Q ++ YT A+ A PG SEHQ GLA+DI N DG + S E W N+ +GFI RYP ITG ++EPWH RYVG E A ++ G LEEYL ", "sequence_from_db": "ARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDI-NADG---IHSTGNEVY--RWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLN", "sequence_from_broadstreet": "MEKSNYHSNVNHHKRHMKQSGEKRAFLWAFIISFTVCTLFLGWRLVSVLEATQLPPIPATHTGSGTGVAENPEENTLATAKEQGDEQEWSLILVNRQNPIPAQYDVELEQLSNGERIDIRISPYLQDLFDAARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLNTEK", "dna_sequence_from_broadstreet": "ATGGAAAAAAGCAACTATCATTCCAATGTGAATCATCACAAACGGCATATGAAACAATCTGGGGAAAAACGGGCTTTTCTATGGGCGTTCATTATCTCGTTCACAGTCTGCACGCTGTTTTTGGGGTGGAGATTGGTTTCCGTATTGGAGGCAACACAGCTACCGCCCATCCCTGCAACTCATACAGGCAGCGGGACTGGTGTAGCGGAGAATCCAGAGGAAAACACTCTTGCCACCGCCAAAGAACAGGGAGATGAACAGGAATGGAGCCTGATTTTAGTGAACAGGCAGAACCCCATCCCCGCCCAGTACGATGTGGAACTTGAGCAGCTGTCAAATGGTGAGCGGATAGACATTCGGATTTCTCCCTACCTCCAGGATTTGTTTGATGCCGCAAGAGCTGATGGAGTTTACCCGATTGTCGCATCCGGATACCGGACAACAGAAAAACAGCAAGAAATCATGGATGAAAAAGTCGCCGAATACAAGGCGAAAGGCTACACCTCTGCACAGGCTAAAGCGGAAGCAGAAACTTGGGTGGCCGTGCCGGGAACAAGCGAGCATCAGCTTGGTCTTGCTGTGGATATCAATGCGGATGGAATTCATTCAACCGGCAACGAGGTTTACAGATGGCTGGATGAAAACAGCTATCGCTTTGGTTTTATTCGCCGCTACCCGCCAGACAAGACAGAGATAACCGGTGTGAGCAACGAGCCGTGGCATTACCGATATGTCGGCATCGAAGCTGCCACAAAGATATACCACCAAGGGCTTTGCCTTGAGGAATATTTAAACACAGAAAAATGA", "partial": "0", "query_start": 37, "query_end": 429, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 40.0}}} diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt new file mode 100644 index 0000000..1f16da6 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt @@ -0,0 +1,3 @@ +ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note +k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588 k141_1197_2 683 1345 + Strict 200 326.635 vanX gene in vanO cluster 75.25 3002954 protein homolog model n/a n/a glycopeptide antibiotic antibiotic target alteration vanX; glycopeptide resistance gene cluster ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT 108.91 gnl|BL_ORD_ID|1672|hsp_num:0 1699 +k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658 k141_10683_1 1 453 + Strict 50 90.8929 vanY gene in vanM cluster 38.62 3002961 protein homolog model n/a n/a glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR 64.38 gnl|BL_ORD_ID|1673|hsp_num:0 1713 diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json new file mode 100644 index 0000000..d49ca4d --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json @@ -0,0 +1 @@ +{"k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588": {"gnl|BL_ORD_ID|1672|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanO cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1699", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002954", "ARO_name": "vanX gene in vanO cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 5.8564e-116, "bit_score": 326.635, "max_identities": 152, "cvterm_id": "36897", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "M DFV+VD+ VPGVRWDAKYAT DNFTGKPV+GYLANRIVGTRALC+ALE R++AAS GFGLLLWDGYRP+RAVDSFL W++QPEDG TK+RHYPNI R EM E+GYVA++SGHSRG VDLTLY L TG+L PMGG HDLMD ISHH A GI E+ NR LRS+ME CGF YD EWWHYTLK EPYPD YFDFP+T", "sequence_from_db": "MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT", "sequence_from_broadstreet": "MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT", "dna_sequence_from_broadstreet": "ATGAACGACGACTTCGTCTACGTCGACGACTGGGTGCCCGGAGTCCGCTGGGATGCCAAGTACGCCACGTGGGACAACTTCACCGGCAAACCGGTAGACGGCTACCTCGCGAATCGAATCGTCGGCACCCGGGCTTTGTGCGCGGCCCTCGAGCAAGCACGCGAGAAGGCAGCTTCCCTCGGCTTCGGATTGCTTCTCTGGGACGGCTACCGTCCTCGACGCGCCGTCGACAGCTTCCTACGCTGGTCAGAACAGCCGGAGGATGGCCAGACGAAGCAGCGACACTATCCCAATATCGACAGACCCGAGATGCTCGAAAAGGGATACGTGGCAACCCAGTCGGGCCACAGTAGGGGCGGCGCCGTTGACCTGACGCTCTATCACCTTGCGACCGGTGAACTTGCTCCTATGGGTGGCGACCACGACCTCATGGACCCGATCTCACATCATCGAGCGCGAGGAATCAAGCCAATCGAGTCCAAGAATCGTGAGCTTCTTCGTTCCATCATGGAGGACTGCGGATTTGATCGGTACGACTGCGAGTGGTGGCACTACACGCTGAAACGCGAACCATATCCAGATGTCTACTTCGACTTTCCGATCACGTGA", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 75.25}, "gnl|BL_ORD_ID|2066|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanI cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "2243", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3003725", "ARO_name": "vanX gene in vanI cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.67433e-112, "bit_score": 317.39, "max_identities": 147, "cvterm_id": "42687", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "MK DFVFVDE V G+RWDAKYAT DNFTGKPV+GY ANRIVGTRALC+ALE R+ AAS GFGLLLWDGYRPQ AVD FL W+KQPEDG TK++HYPNI R+E+ E+GYVA+KSGHSRGS +DLTLY L +G LVPMGG DLMD +SHHGA GI++AE NR L S+MEA GF SY EWWHY+LK+EPYP+TYFDF + ", "sequence_from_db": "MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA", "sequence_from_broadstreet": "MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA", "dna_sequence_from_broadstreet": "ATGAAAAGTGATTTTGTCTTTGTGGACGAGTTGGTATCAGGAATACGTTGGGATGCTAAATACGCCACCTGGGATAATTTTACCGGCAAACCGGTGGACGGCTATGCAGCCAATCGAATTGTCGGTACGAGAGCGTTGTGCGCGGCCTTGGAAAAAGCACGGGAAAACGCCGCATCCTTGGGCTTTGGCTTGCTTCTTTGGGATGGTTACCGCCCTCAATGCGCCGTAGATTGCTTTCTGCGCTGGTCTAAACAGCCGGAAGATGGCCGGACGAAACAGAAACACTATCCGAATATTGACCGATCCGAGATCATCGAAAAAGGATATGTGGCTGCCAAGTCGGGCCACAGCCGGGGCAGCGCCATTGATTTAACCCTTTATCATTTAGCTTCCGGAACACTTGTGCCCATGGGCGGTGATTTTGATTTGATGGATTCAGTCTCACATCATGGCGCACATGGAATCAGCCAAGCCGAAGCGAGAAACCGTCAATATCTTTGTTCGATCATGGAGGCCAGCGGTTTTGTTTCCTACGCTTGCGAGTGGTGGCATTACAGCCTGAAACACGAACCTTATCCCAACACTTACTTTGATTTTCTCATCGCCTAG", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 72.77}, "gnl|BL_ORD_ID|1499|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanF cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1509", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002952", "ARO_name": "vanX gene in vanF cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.33452e-99, "bit_score": 286.189, "max_identities": 134, "cvterm_id": "39542", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ DFVF+DE + GVRWD+KYAT DNFTGKPV+GY NRI GT AL AL V+++AA+ G+GLLLWDGYRPQRAV+ FLHW+ QPEDG TK R+YPNI R EM +GYVASKS HSRGS +DLTLY L TG LVPMG G D MDE SHH + GI+ E NR L S+ME GF SY EWWHY L+NEPYP +YFDFP+", "sequence_from_db": "MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPI", "sequence_from_broadstreet": "MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPIGGNHLDPFSNFCGTVPLDALSP", "dna_sequence_from_broadstreet": "ATGGAAAAAGATTTTGTTTTTTTAGATGAAATATTGCATGGAGTTCGTTGGGACTCCAAATATGCCACATGGGACAATTTCACTGGAAAACCGGTAGACGGATATGAAGTCAATCGCATAGCGGGGACATATGCTTTGGCTGTTGCGCTGCTGGAGGTAAAGAAGCAGGCGGCTGCTCTAGGGTACGGCTTGCTCCTGTGGGATGGCTATCGTCCTCAACGTGCGGTAAACTGTTTCTTGCATTGGTCTGCGCAGCCGGAAGACGGCCGCACAAAAGAAAGATATTATCCCAATATTGATCGGATCGAGATGGTTACAAAGGGATATGTGGCTTCAAAATCAAGCCACAGTCGCGGAAGCGCGATTGACCTTACGCTTTATCGATTGGACACGGGTGCGCTTGTCCCTATGGGGAGCGGCTTCGATTTTATGGATGAACGTTCACATCATACCTCAAAAGGAATTTCAAGTAACGAAGCGCAAAATCGCCAGTTATTATGTTCTATTATGGAATACAGCGGATTTGAATCATATGTATATGAATGGTGGCACTACGTATTAAGAAACGAACCATACCCCAGCAGCTATTTTGATTTTCCCATTGGCGGGAACCATCTAGACCCATTTTCCAACTTTTGTGGGACAGTGCCACTTGATGCGTTGTCGCCCTAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 66.67}, "gnl|BL_ORD_ID|4672|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanA cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "217", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002949", "ARO_name": "vanX gene in vanA cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.30871e-95, "bit_score": 274.633, "max_identities": 127, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ F F+DE V GVRWDAKYAT DNFTGKPV+GY NRIVGT L +L ++ AA++G+GLLLWDGYRP+RAV+ F+ WA QPE+ TK +YPNI R EM +GYVASKS HSRGS +DLTLY L TG+LVPMG D MDE SHH A GI+ E NR LRS+ME GF +Y EWWHY L++EPYP++YFDFPV", "sequence_from_db": "MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPV", "sequence_from_broadstreet": "MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK", "dna_sequence_from_broadstreet": "ATGGAAATAGGATTTACTTTTTTAGATGAAATAGTACACGGTGTTCGTTGGGACGCTAAATATGCCACTTGGGATAATTTCACCGGAAAACCGGTTGACGGTTATGAAGTAAATCGCATTGTAGGGACATACGAGTTGGCTGAATCGCTTTTGAAGGCAAAAGAACTGGCTGCTACCCAAGGGTACGGATTGCTTCTATGGGACGGTTACCGTCCTAAGCGTGCTGTAAACTGTTTTATGCAATGGGCTGCACAGCCGGAAAATAACCTGACAAAGGAAAGTTATTATCCCAATATTGACCGAACTGAGATGATTTCAAAAGGATACGTGGCTTCAAAATCAAGCCATAGCCGCGGCAGTGCCATTGATCTTACGCTTTATCGATTAGACACGGGTGAGCTTGTACCAATGGGGAGCCGATTTGATTTTATGGATGAACGCTCTCATCATGCGGCAAATGGAATATCATGCAATGAAGCGCAAAATCGCAGACGTTTGCGCTCCATCATGGAAAACAGTGGGTTTGAAGCATATAGCCTCGAATGGTGGCACTATGTATTAAGAGACGAACCATACCCCAATAGCTATTTTGATTTCCCCGTTAAATAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.18}, "gnl|BL_ORD_ID|1647|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanB cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1666", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002950", "ARO_name": "vanX gene in vanB cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.96956e-95, "bit_score": 274.248, "max_identities": 128, "cvterm_id": "35918", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVT", "match": "M+ F+F+DE + GVRWDAKYAT DNFTGKPV+GY NRI+GT+A+ AL + AA G+GLLLWDGYRP+ AVD FL WA QPED TK ++YPNI RAE+ +GYVAS+S HSRGST+DLTLY L TG+LV MG D MDE SHH A GI AE NR LR +ME+ GF SY EWWHY L +EPYPDTYF+F V+", "sequence_from_db": "MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS", "sequence_from_broadstreet": "MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS", "dna_sequence_from_broadstreet": "ATGGAAAATGGTTTTTTGTTTTTAGATGAAATGTTGCATGGTGTTCGTTGGGATGCCAAGTACGCTACATGGGATAACTTCACGGGAAAACCAGTGGATGGGTATGAGGTGAATCGCATCATCGGCACAAAGGCCGTGGCGCTTGCTCTGCGCGAAGCACAAATCCATGCGGCACGCCTTGGCTACGGCTTGCTTTTATGGGATGGATATCGGCCAAAATCTGCGGTGGACTGTTTCCTGCGTTGGGCGGCGCAGCCGGAGGACAACCTCACAAAAGAAAAATATTACCCCAATATTGAGCGAGCCGAGTTGATTACAAAGGGCTATGTGGCCTCACAATCCAGCCATAGCCGTGGAAGCACAATTGATCTTACGCTCTACCACTTGGATACAGGGGAACTTGTTTCAATGGGAAGCAACTTCGATTTTATGGACGAACGGTCGCACCATACAGCAAAAGGGATAGGGAATGCAGAGGCACAAAATCGAAGATGCTTGCGTAAAATCATGGAAAGCAGCGGATTTCAGTCCTATCGCTTTGAATGGTGGCACTATAAGTTGATTGATGAGCCATACCCCGATACCTATTTTAATTTTGCTGTTTCATAA", "partial": "0", "query_start": 683, "query_end": 1288, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.37}, "gnl|BL_ORD_ID|1502|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanD cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1566", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3003070", "ARO_name": "vanX gene in vanD cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 3.44626e-94, "bit_score": 271.552, "max_identities": 125, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ +FVF+DE +PG+RWDAKYAT DNFTGKPV+GY NRIVGT+ L +AL ++ A G+GLLLWDGYRPQ AVD FL WA PE+ TK+R+YPNI R EM +GYVAS+S HSRGS +DLT++ L TG LVPMGG D MD SHH A G++ E GNR LR +ME GF +Y EWWHY L +EPYPDTYFDF +", "sequence_from_db": "MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCI", "sequence_from_broadstreet": "MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCIA", "dna_sequence_from_broadstreet": "ATGGAAAAGAACTTTGTCTTTTTGGATGAAATGCTGCCGGGCATCCGGTGGGATGCCAAATATGCCACATGGGACAATTTCACCGGGAAACCGGTAGACGGATACGAGGTAAACCGCATTGTGGGAACGAAAGAGCTTGGTGCCGCTTTACGTAAGGCACAGAAGGCGGCGGAGAAACTGGGATACGGTCTGCTCTTATGGGACGGCTACCGTCCCCAGTGTGCAGTGGACTGCTTTTTGACTTGGGCTTCCCTGCCGGAGAACAATCTGACGAAAAAGCGTTACTACCCAAATATCAAAAGGAACGAGATGATCACGAAAGGGTATGTGGCTTCTCAGTCCAGCCACAGTCGCGGGAGCGCGATTGATCTCACGATTTTTCGTTTGGACACGGGTATGCTTGTGCCAATGGGCGGAGATTTCGACTTTATGGATGTACGGTCGCATCATGCCGCCAGTGGTCTGAGCGAAGAGGAGGCCGGAAACCGTGAGCGCCTGCGTGATATCATGGAGCGCAGCGGATTTGAAGCCTACCGATATGAATGGTGGCATTATGTCTTGGCAGACGAGCCATACCCGGATACATATTTTGATTTTTGCATTGCCTAG", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 62.19}, "gnl|BL_ORD_ID|4822|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanP cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "5806", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3007190", "ARO_name": "vanX gene in vanP cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 5.82743e-94, "bit_score": 271.166, "max_identities": 121, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "MK +FV++DE +PGVRWDAKYAT DNF G PV GY NR+VGT + AL+ V + A +G GLLLWDGYRP RAV F+ W K+ +D + K +HYP+I + M E GY+A SGHSRGST+DLTLYDL + L+ MGG DLMDEISH+ A GIT+ E NR LR LM CGF Y++EWWHY+LK+EPYPDTYFDF +", "sequence_from_db": "MKSEFVYLDEVIPGVRWDAKYATWDNFMGMPVNGYQVNRVVGTVEMADALKEVSKLAKEKGVGLLLWDGYRPVRAVSHFMEWVKKSKDESRKAKHYPHIDKKTMIEEGYIAEYSGHSRGSTIDLTLYDLESKKLLDMGGDFDLMDEISHYAAEGITKEEKENRKLLRDLMVKCGFVPYENEWWHYSLKDEPYPDTYFDFVI", "sequence_from_broadstreet": "MKSEFVYLDEVIPGVRWDAKYATWDNFMGMPVNGYQVNRVVGTVEMADALKEVSKLAKEKGVGLLLWDGYRPVRAVSHFMEWVKKSKDESRKAKHYPHIDKKTMIEEGYIAEYSGHSRGSTIDLTLYDLESKKLLDMGGDFDLMDEISHYAAEGITKEEKENRKLLRDLMVKCGFVPYENEWWHYSLKDEPYPDTYFDFVIE", "dna_sequence_from_broadstreet": "ATGAAATCAGAATTTGTTTATTTGGATGAAGTAATACCGGGAGTAAGATGGGATGCAAAATATGCTACTTGGGATAATTTTATGGGAATGCCTGTTAATGGTTATCAGGTCAATCGTGTTGTAGGTACAGTTGAGATGGCAGATGCCTTAAAGGAGGTCAGTAAGCTTGCAAAGGAAAAGGGCGTTGGTTTACTTTTGTGGGATGGATACCGTCCTGTCCGTGCGGTTTCCCACTTTATGGAATGGGTAAAAAAGAGTAAAGATGAAAGCCGTAAGGCGAAGCATTATCCACATATTGATAAAAAGACGATGATAGAGGAAGGCTACATTGCAGAGTATTCCGGTCACAGCAGGGGAAGTACGATTGATTTGACACTGTATGATTTGGAAAGCAAAAAGCTTCTGGACATGGGTGGGGATTTTGATTTGATGGACGAAATCTCCCACTATGCGGCAGAGGGGATTACCAAGGAAGAGAAGGAGAATCGTAAATTACTTCGGGATTTGATGGTCAAATGCGGATTTGTTCCATATGAAAATGAATGGTGGCATTATTCGTTAAAAGACGAGCCATATCCGGATACATATTTTGACTTTGTCATTGAATAG", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 60.2}, "gnl|BL_ORD_ID|1951|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 683, "orf_end": 1345, "orf_from": "k141_1197_2", "model_name": "vanX gene in vanM cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1996", "pass_evalue": "n/a", "pass_bitscore": "200", "ARO_accession": "3002953", "ARO_name": "vanX gene in vanM cluster", "ARO_category": {"36020": {"category_aro_accession": "3000011", "category_aro_cvterm_id": "36020", "category_aro_name": "vanX", "category_aro_description": "VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 7.41369e-94, "bit_score": 270.781, "max_identities": 127, "cvterm_id": "36779", "query": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPV", "match": "M+ F F+DE + VRWDAKYAT DNFTGKP++GY NRI+GT L AL V++ A ++G+GLLLWDGYRPQ+AV+ FL WA QPED TK ++YPNI R EM +GYVASKS HSRGS +DLTLY L T +LVPMG G D MDE SHH A GIT E NR LRS+ME GF +Y EWWHY L NEPYP + FDFPV", "sequence_from_db": "MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPV", "sequence_from_broadstreet": "MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPVK", "dna_sequence_from_broadstreet": "ATGGAAAAAGGATTTACCTTTTTAGATGAAATATTAAACGATGTTCGTTGGGACGCTAAATATGCTACGTGGGACAACTTCACTGGAAAACCAATTGATGGATATGAAGTAAATCGAATTATAGGAACATATGAGTTAGCCGATGCGCTATTGAAGGTTCAAGAATTAGCTTTTAACCAAGGTTATGGATTGCTTTTATGGGACGGTTACCGTCCCCAACAAGCTGTAAATTGTTTTTTGCAATGGGCGGCACAGCCGGAAGATAATCGAACAAAGGCAAAATATTATCCCAATATTGACCGAACTGAGATGGTTTCAAAAGGATACGTGGCTTCAAAATCAAGTCATAGCCGCGGAAGTGCAATTGATCTTACACTTTATCGATTAGACACGGACGAACTTGTTCCGATGGGGAGCGGATTTGATTTTATGGATGAGCGCTCTCATCATGAGGCAAAAGGAATTACGAGCAATGAAGCGCAAAACCGTAGATTTTTGCGTTCCATTATGGAAAACAGTGGGTTTGAAGCGTATAGTTTCGAATGGTGGCACTATGTATTGATAAACGAACCTTATCCCTATAGCTGCTTTGATTTTCCTGTCAAATAA", "partial": "0", "query_start": 683, "query_end": 1285, "orf_dna_sequence": "ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG", "orf_prot_sequence": "MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA", "perc_identity": 63.18}}, "k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658": {"gnl|BL_ORD_ID|1673|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanM cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1713", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002961", "ARO_name": "vanY gene in vanM cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 4.74333e-24, "bit_score": 90.8929, "max_identities": 56, "cvterm_id": "36779", "query": "EAAGAYRQMAAEAGAAGVP-MSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGL", "match": "+ A + +M A GV S SGFR EQ+ LY ++ A GYSEH GLA+DI G+ +E +E G W NA YGFI+RYP ITG +EPWH RYVG H+ + + LEEYL ", "sequence_from_db": "KVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPA--------GYSEHNLGLALDI----GSTQME--MSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDF", "sequence_from_broadstreet": "MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR", "dna_sequence_from_broadstreet": "ATGGTCTTTCAAGGAAACTTACTCTTGGTTAATAACGAATATCCGGTTCTCGAAGAGAGTATAAAAACAGACGTTGTAAATTTATTTAAACATGATGAATTGACAAAAGGATATGAATTGCTCAATAGGGAAATTTATTTATCGGAGAAAGTTGCCCGTGAATTTTCAGAGATGGTAGATGCGGCTGAAAAAGAAGGAGTTCGCCATTTTTCAATCAATAGTGGGTTTCGAAACTTTGATGAGCAAAATGCCCTTTATCAAGAAATGGGGTCTGACTACGCCTTGCCTGCAGGTTATAGCGAACATAATTTAGGTTTAGCACTTGATATCGGATCTACTCAAATGGAAATGAGTGAGGCACCGGAAGGAAAGTGGCTAGAAGATAATGCGTGGGAATACGGCTTTATTTTACGCTATCCAATGGACAAAACGGCCATCACAGGTATTCAGTATGAACCTTGGCATTTTCGCTATGTGGGATTACCGCACAGTGCAATTATAGAGGAAAAGAATTTTGCTTTAGAAGAATATTTGGATTTCCTAAAAGAACAAAAATCCATTTCAGGTACTATACATGGCGAAAATTATGAGATTTCTTATTATCCTATTACCGAAAAAACAGACATTGAAATGCCTGCCAATCTTCATTATGAAATATCAGGAAACAATATGGATGGTGTGATTGTGACAGTGTATCGCTAA", "partial": "0", "query_start": 1, "query_end": 432, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 38.62}, "gnl|BL_ORD_ID|1808|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanF cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "1899", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002958", "ARO_name": "vanY gene in vanF cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.41093e-23, "bit_score": 90.8929, "max_identities": 53, "cvterm_id": "39542", "query": "EAAGAYRQMAAEAGAAGVPMSAVS-GFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "E AG + +M A A GV +S G+R EQ +LY +F A G+SEH GL++D+ G+ ++ A G W N YGFI+RYP +TG +EPWH+RYVG H+ M + LEEYL", "sequence_from_db": "EIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPA--------GHSEHNLGLSLDV----GSTQMKMDKAP--EGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYL", "sequence_from_broadstreet": "MKKWGLLLVFALFLVFIFNILPISQDKVEDRIYEQNDKDTSDDKMTAENMQKIELTEEQIYQGNLLLVNNEHPVHQKSIKSDIINLFTHKELTKGYGLLDNEIKLSEEIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPAGHSEHNLGLSLDVGSTQMKMDKAPEGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYLDYLKEEKSISVRVDGKKYTISYDPISQNETIEVEVPADEQYEISGNNIDGVIVTTFS", "dna_sequence_from_broadstreet": "ATGAAAAAGTGGGGACTTTTATTGGTTTTTGCATTATTTCTAGTATTTATTTTTAATATATTACCGATATCCCAAGATAAAGTAGAGGATCGAATATATGAACAAAATGACAAAGATACATCGGATGATAAAATGACAGCTGAAAATATGCAAAAGATTGAGCTTACGGAAGAGCAGATCTATCAAGGGAATCTACTCTTGGTCAACAATGAACATCCTGTTCACCAAAAGAGTATAAAATCGGATATTATAAATTTATTTACGCACAAAGAATTGACAAAGGGGTATGGGTTACTTGATAACGAAATTAAATTGTCAGAGGAAATAGCTGGGAAATTTTCAGAGATGATAGCTGCGGCTGAAGAGGATGGCGTTAGTAATTTTTTAATTAGCAGTGGTTATCGAGACTTGGATGAGCAAAGCAGACTTTATGAGGAAATGGGTTCTGATTTTGCTTTGCCAGCAGGTCATAGTGAACACAACTTGGGGTTATCGCTTGATGTAGGATCTACTCAAATGAAGATGGATAAAGCGCCTGAAGGAAAGTGGATAGAAAAAAATTGTTGGGAATACGGCTTTATATTACGCTATCCCTTGGATAAAACGGATGTTACAGGAATTCAATATGAACCTTGGCATATTCGCTATGTCGGTTTGCCTCACAGTGCGATTATGCAGGAAATGAATTTAGCTTTGGAAGAATATTTAGATTATTTAAAAGAAGAAAAGAGCATTTCTGTTCGTGTTGATGGGAAAAAATATACAATTTCATATGATCCCATTTCTCAAAACGAGACAATTGAAGTTGAAGTACCAGCGGATGAACAGTATGAAATATCTGGTAATAATATTGATGGAGTAATTGTGACCACATTTTCTTGA", "partial": "0", "query_start": 1, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 37.06}, "gnl|BL_ORD_ID|4732|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanG cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "298", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002959", "ARO_name": "vanY gene in vanG cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 6.26485e-23, "bit_score": 88.5817, "max_identities": 56, "cvterm_id": "35918", "query": "AAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPE---------AADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "A E +PM VSG+RT +Q LY F E A+ A PG+SEHQ G A+DI L W N+ YGFI RYP ITG A E WH RYVG E A M++ G LEEYL", "sequence_from_db": "AREENWGELPM-VVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYL-----------WLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYL", "sequence_from_broadstreet": "MNHMNMKHRRRKRRRNQSFLFTGILLLVVVSASSFLWYGFGNAAKKDSVIEEMPFTITQDGMQAKEEIKKTVLETSYGGKQQVAEENHGNTQNAGTDEAWNLMLVNRDNAIPDNYEVNLVEVEGGERVDERIYEPLMEMLNAAREENWGELPMVVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYLWLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYLEKKQSEN", "dna_sequence_from_broadstreet": "ATGAACCATATGAATATGAAACACAGACGCAGAAAACGCAGACGTAACCAATCTTTTTTGTTCACAGGAATTTTACTCTTAGTTGTAGTATCTGCAAGCAGTTTTTTATGGTACGGTTTTGGCAATGCGGCAAAAAAAGACAGTGTTATTGAAGAAATGCCATTTACCATTACACAGGACGGAATGCAGGCAAAGGAAGAAATAAAGAAAACGGTACTGGAAACTTCCTATGGCGGCAAACAGCAGGTAGCGGAAGAAAATCACGGCAATACACAAAATGCAGGGACAGACGAAGCGTGGAATTTAATGCTTGTCAACAGAGATAATGCGATTCCAGACAATTACGAAGTAAATCTGGTCGAAGTAGAGGGCGGGGAGCGTGTAGATGAGCGTATCTATGAACCTCTTATGGAAATGCTTAATGCGGCAAGGGAGGAAAACTGGGGCGAATTGCCGATGGTAGTATCTGGCTATCGGACGCAGGAAAAACAGCAGAGCCTTTATGATGAAAAGATTGCAAAGTTCAAAAAAGAGGGGTATTCAGACAGTGAAGCCGTAAGGCAGGCAGAACAATGGGTTGCAGTGCCAGGTCACAGTGAGCATCAGCTCGGTTTTGCAGTGGATATTAACGGGGCAACTTATGATGTTTATCTATGGTTGCAGGAAAACAGCTATAAATACGGCTTTATCTTCAGATATCCCGGCAGTAAAACGGATATTACCGGGACTGCTGAAGAAGTATGGCATTACCGTTATGTTGGAGTGGAAGCGGCAACTGAAATGTATGAAAATGGATTATGTCTTGAGGAATATCTTGAGAAAAAGCAATCAGAAAACTAA", "partial": "0", "query_start": 28, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 39.44}, "gnl|BL_ORD_ID|4669|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanA cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "89", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002955", "ARO_name": "vanY gene in vanA cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "35948": {"category_aro_accession": "0000029", "category_aro_cvterm_id": "35948", "category_aro_name": "teicoplanin", "category_aro_description": "Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation and transpeptidation.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 3.428e-22, "bit_score": 87.0409, "max_identities": 52, "cvterm_id": "36779", "query": "EAAGAYRQMAAEAGAAGVPMSAV-SGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYL", "match": "E A + +M +A GV + SG+R EQ LY + G E A GYSEH +GL++D+ + +E G W NA YGFI+RYP +TG +EPWH+RYVG H+ M + LEEY+", "sequence_from_db": "EIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLY----QEMGAEYA----LPAGYSEHNSGLSLDVGS--SLTKMERA----PEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYM", "sequence_from_broadstreet": "MKKLFFLLLLLFLIYLGYDYVNEALFSQEKVEFQNYDQNPKEHLENSGTSENTQEKTITEEQVYQGNLLLINSKYPVRQESVKSDIVNLSKHDELINGYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLYQEMGAEYALPAGYSEHNSGLSLDVGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYMDYLKEEKTISVSVNGEKYEIFYYPVTKNTTIHVPTNLRYEISGNNIDGVIVTVFPGSTHTNSRR", "dna_sequence_from_broadstreet": "ATGAAGAAGTTGTTTTTTTTATTGTTATTGTTATTCTTAATATACTTAGGTTATGACTACGTTAATGAAGCACTGTTTTCTCAGGAAAAAGTCGAATTTCAAAATTATGATCAAAATCCCAAAGAACATTTAGAAAATAGTGGGACTTCTGAAAATACCCAAGAGAAAACAATTACAGAAGAACAGGTTTATCAAGGAAATCTGCTATTAATCAATAGTAAATATCCTGTTCGCCAAGAAAGTGTGAAGTCAGATATCGTGAATTTATCTAAACATGACGAATTAATAAATGGATACGGGTTGCTTGATAGTAATATTTATATGTCAAAAGAAATAGCACAAAAATTTTCAGAGATGGTCAATGATGCTGTAAAGGGTGGCGTTAGTCATTTTATTATTAATAGTGGCTATCGAGACTTTGATGAGCAAAGTGTGCTTTACCAAGAAATGGGGGCTGAGTATGCCTTACCAGCAGGTTATAGTGAGCATAATTCAGGTTTATCACTAGATGTAGGATCAAGCTTGACGAAAATGGAACGAGCCCCTGAAGGAAAGTGGATAGAAGAAAATGCTTGGAAATACGGGTTCATTTTACGTTATCCAGAGGACAAAACAGAGTTAACAGGAATTCAATATGAACCATGGCATATTCGCTATGTTGGTTTACCACATAGTGCGATTATGAAAGAAAAGAATTTCGTTCTCGAGGAATATATGGATTACCTAAAAGAAGAAAAAACCATTTCTGTTAGTGTAAATGGGGAAAAATATGAGATCTTTTATTATCCTGTTACTAAAAATACCACCATTCATGTGCCGACTAATCTTCGTTATGAGATATCAGGAAACAATATAGACGGTGTAATTGTGACAGTGTTTCCCGGATCAACACATACTAATTCAAGGAGGTAA", "partial": "0", "query_start": 1, "query_end": 426, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 36.36}, "gnl|BL_ORD_ID|602|hsp_num:0": {"type_match": "Strict", "orf_strand": "+", "orf_start": 1, "orf_end": 453, "orf_from": "k141_10683_1", "model_name": "vanY gene in vanB cluster", "model_type": "protein homolog model", "model_type_id": 40292, "model_id": "556", "pass_evalue": "n/a", "pass_bitscore": "50", "ARO_accession": "3002956", "ARO_name": "vanY gene in vanB cluster", "ARO_category": {"36216": {"category_aro_accession": "3000077", "category_aro_cvterm_id": "36216", "category_aro_name": "vanY", "category_aro_description": "VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.", "category_aro_class_name": "AMR Gene Family"}, "36373": {"category_aro_accession": "3000234", "category_aro_cvterm_id": "36373", "category_aro_name": "glycopeptide resistance gene cluster", "category_aro_description": "Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria. This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 1.3754e-20, "bit_score": 82.4185, "max_identities": 56, "cvterm_id": "35918", "query": "AGAAGVPMSAVSGFRTGAEQDQLY---------VSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLG", "match": "A A GV SG+RT +Q ++ YT A+ A PG SEHQ GLA+DI N DG + S E W N+ +GFI RYP ITG ++EPWH RYVG E A ++ G LEEYL ", "sequence_from_db": "ARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDI-NADG---IHSTGNEVY--RWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLN", "sequence_from_broadstreet": "MEKSNYHSNVNHHKRHMKQSGEKRAFLWAFIISFTVCTLFLGWRLVSVLEATQLPPIPATHTGSGTGVAENPEENTLATAKEQGDEQEWSLILVNRQNPIPAQYDVELEQLSNGERIDIRISPYLQDLFDAARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLNTEK", "dna_sequence_from_broadstreet": "ATGGAAAAAAGCAACTATCATTCCAATGTGAATCATCACAAACGGCATATGAAACAATCTGGGGAAAAACGGGCTTTTCTATGGGCGTTCATTATCTCGTTCACAGTCTGCACGCTGTTTTTGGGGTGGAGATTGGTTTCCGTATTGGAGGCAACACAGCTACCGCCCATCCCTGCAACTCATACAGGCAGCGGGACTGGTGTAGCGGAGAATCCAGAGGAAAACACTCTTGCCACCGCCAAAGAACAGGGAGATGAACAGGAATGGAGCCTGATTTTAGTGAACAGGCAGAACCCCATCCCCGCCCAGTACGATGTGGAACTTGAGCAGCTGTCAAATGGTGAGCGGATAGACATTCGGATTTCTCCCTACCTCCAGGATTTGTTTGATGCCGCAAGAGCTGATGGAGTTTACCCGATTGTCGCATCCGGATACCGGACAACAGAAAAACAGCAAGAAATCATGGATGAAAAAGTCGCCGAATACAAGGCGAAAGGCTACACCTCTGCACAGGCTAAAGCGGAAGCAGAAACTTGGGTGGCCGTGCCGGGAACAAGCGAGCATCAGCTTGGTCTTGCTGTGGATATCAATGCGGATGGAATTCATTCAACCGGCAACGAGGTTTACAGATGGCTGGATGAAAACAGCTATCGCTTTGGTTTTATTCGCCGCTACCCGCCAGACAAGACAGAGATAACCGGTGTGAGCAACGAGCCGTGGCATTACCGATATGTCGGCATCGAAGCTGCCACAAAGATATACCACCAAGGGCTTTGCCTTGAGGAATATTTAAACACAGAAAAATGA", "partial": "0", "query_start": 37, "query_end": 429, "orf_dna_sequence": "GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA", "orf_prot_sequence": "EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY", "perc_identity": 40.0}}} diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt new file mode 100644 index 0000000..dbf3c40 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt @@ -0,0 +1,3 @@ +ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note +k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588 k141_1197_2 683 1345 + Strict 200 326.635 vanX gene in vanO cluster 75.25 3002954 protein homolog model n/a n/a glycopeptide antibiotic antibiotic target alteration vanX; glycopeptide resistance gene cluster ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT 108.91 gnl|BL_ORD_ID|1674|hsp_num:0 1699 +k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658 k141_10683_1 1 453 + Strict 50 90.8929 vanY gene in vanM cluster 38.62 3002961 protein homolog model n/a n/a glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR 64.38 gnl|BL_ORD_ID|1675|hsp_num:0 1713 diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt new file mode 100644 index 0000000..8add729 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt @@ -0,0 +1,5 @@ +Reference Sequence ARO Term ARO Accession Reference Model Type Reference DB Reference Allele Source Resistomes & Variants: Observed in Genome(s) Resistomes & Variants: Observed in Plasmid(s) Resistomes & Variants: Observed Pathogen(s) Completely Mapped Reads Mapped Reads with Flanking Sequence All Mapped Reads Percent Coverage Length Coverage (bp) Average MAPQ (Completely Mapped Reads) Mate Pair Linkage Reference Length AMR Gene Family Drug Class Resistance Mechanism +ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1 mdtF 3000796 protein homolog model CARD CARD curation no data no data Escherichia coli 2 0 2 8.09 252 193.00 * 3114 resistance-nodulation-cell division (RND) antibiotic efflux pump macrolide antibiotic; fluoroquinolone antibiotic; penam antibiotic efflux +ARO:3000815|ID:154|Name:mgrA|NCBI:BA000018.3 mgrA 3000815 protein homolog model CARD CARD curation no data no data Staphylococcus aureus 1 0 1 19.59 87 172.00 * 444 ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics antibiotic efflux +ARO:3000805|ID:172|Name:OprN|NCBI:AE004091.2 OprN 3000805 protein homolog model CARD CARD curation no data no data Pseudomonas aeruginosa 2 0 2 17.76 252 193.00 * 1419 resistance-nodulation-cell division (RND) antibiotic efflux pump fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic antibiotic efflux +ARO:3000026|ID:377|Name:mepA|NCBI:AY661734.1 mepA 3000026 protein homolog model CARD CARD curation no data no data Staphylococcus aureus 2 0 2 17.70 240 190.50 * 1356 multidrug and toxic compound extrusion (MATE) transporter glycylcycline; tetracycline antibiotic antibiotic efflux diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt new file mode 100644 index 0000000..60e7d3b --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt @@ -0,0 +1,17 @@ + +********************************************** +Stats for BAM file(s): +********************************************** + +Total reads: 5000 +Mapped reads: 59 (1.18%) +Forward strand: 685 (13.7%) +Reverse strand: 4315 (86.3%) +Failed QC: 0 (0%) +Duplicates: 0 (0%) +Paired-end reads: 5000 (100%) +'Proper-pairs': 42 (0.84%) +Both pairs mapped: 49 (0.98%) +Read 1: 2500 +Read 2: 2500 +Singletons: 10 (0.2%) diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam new file mode 100644 index 0000000..f2797a6 Binary files /dev/null and b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam differ diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt new file mode 100644 index 0000000..8add729 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt @@ -0,0 +1,5 @@ +Reference Sequence ARO Term ARO Accession Reference Model Type Reference DB Reference Allele Source Resistomes & Variants: Observed in Genome(s) Resistomes & Variants: Observed in Plasmid(s) Resistomes & Variants: Observed Pathogen(s) Completely Mapped Reads Mapped Reads with Flanking Sequence All Mapped Reads Percent Coverage Length Coverage (bp) Average MAPQ (Completely Mapped Reads) Mate Pair Linkage Reference Length AMR Gene Family Drug Class Resistance Mechanism +ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1 mdtF 3000796 protein homolog model CARD CARD curation no data no data Escherichia coli 2 0 2 8.09 252 193.00 * 3114 resistance-nodulation-cell division (RND) antibiotic efflux pump macrolide antibiotic; fluoroquinolone antibiotic; penam antibiotic efflux +ARO:3000815|ID:154|Name:mgrA|NCBI:BA000018.3 mgrA 3000815 protein homolog model CARD CARD curation no data no data Staphylococcus aureus 1 0 1 19.59 87 172.00 * 444 ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics antibiotic efflux +ARO:3000805|ID:172|Name:OprN|NCBI:AE004091.2 OprN 3000805 protein homolog model CARD CARD curation no data no data Pseudomonas aeruginosa 2 0 2 17.76 252 193.00 * 1419 resistance-nodulation-cell division (RND) antibiotic efflux pump fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic antibiotic efflux +ARO:3000026|ID:377|Name:mepA|NCBI:AY661734.1 mepA 3000026 protein homolog model CARD CARD curation no data no data Staphylococcus aureus 2 0 2 17.70 240 190.50 * 1356 multidrug and toxic compound extrusion (MATE) transporter glycylcycline; tetracycline antibiotic antibiotic efflux diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt new file mode 100644 index 0000000..60e7d3b --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt @@ -0,0 +1,17 @@ + +********************************************** +Stats for BAM file(s): +********************************************** + +Total reads: 5000 +Mapped reads: 59 (1.18%) +Forward strand: 685 (13.7%) +Reverse strand: 4315 (86.3%) +Failed QC: 0 (0%) +Duplicates: 0 (0%) +Paired-end reads: 5000 (100%) +'Proper-pairs': 42 (0.84%) +Both pairs mapped: 49 (0.98%) +Read 1: 2500 +Read 2: 2500 +Singletons: 10 (0.2%) diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam new file mode 100644 index 0000000..f2797a6 Binary files /dev/null and b/q2_amr/card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam differ diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt new file mode 100644 index 0000000..873522c --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt @@ -0,0 +1,5 @@ +ARO Term ARO Accession Reference Model Type Reference DB Alleles with Mapped Reads Reference Allele(s) Identity to CARD Reference Protein (%) Resistomes & Variants: Observed in Genome(s) Resistomes & Variants: Observed in Plasmid(s) Resistomes & Variants: Observed Pathogen(s) Completely Mapped Reads Mapped Reads with Flanking Sequence All Mapped Reads Average Percent Coverage Average Length Coverage (bp) Average MAPQ (Completely Mapped Reads) Number of Mapped Baits Number of Mapped Baits with Reads Average Number of reads per Bait Number of reads per Bait Coefficient of Variation (%) Number of reads mapping to baits and mapping to complete gene Number of reads mapping to baits and mapping to complete gene (%) Mate Pair Linkage (# reads) Reference Length AMR Gene Family Drug Class Resistance Mechanism +mdtF 3000796 protein homolog model CARD 1 100.0 no data no data Escherichia coli 2.00 0.00 2.00 8.09 252.00 193.00 0 0 0 0 N/A N/A 3114 resistance-nodulation-cell division (RND) antibiotic efflux pump macrolide antibiotic; fluoroquinolone antibiotic; penam antibiotic efflux +mgrA 3000815 protein homolog model CARD 1 100.0 no data no data Staphylococcus aureus 1.00 0.00 1.00 19.59 87.00 172.00 0 0 0 0 N/A N/A 444 ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics antibiotic efflux +OprN 3000805 protein homolog model CARD 1 100.0 no data no data Pseudomonas aeruginosa 2.00 0.00 2.00 17.76 252.00 193.00 0 0 0 0 N/A N/A 1419 resistance-nodulation-cell division (RND) antibiotic efflux pump fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic antibiotic efflux +mepA 3000026 protein homolog model CARD 1 100.0 no data no data Staphylococcus aureus 2.00 0.00 2.00 17.70 240.00 190.50 0 0 0 0 N/A N/A 1356 multidrug and toxic compound extrusion (MATE) transporter glycylcycline; tetracycline antibiotic antibiotic efflux diff --git a/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt b/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt new file mode 100644 index 0000000..873522c --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt @@ -0,0 +1,5 @@ +ARO Term ARO Accession Reference Model Type Reference DB Alleles with Mapped Reads Reference Allele(s) Identity to CARD Reference Protein (%) Resistomes & Variants: Observed in Genome(s) Resistomes & Variants: Observed in Plasmid(s) Resistomes & Variants: Observed Pathogen(s) Completely Mapped Reads Mapped Reads with Flanking Sequence All Mapped Reads Average Percent Coverage Average Length Coverage (bp) Average MAPQ (Completely Mapped Reads) Number of Mapped Baits Number of Mapped Baits with Reads Average Number of reads per Bait Number of reads per Bait Coefficient of Variation (%) Number of reads mapping to baits and mapping to complete gene Number of reads mapping to baits and mapping to complete gene (%) Mate Pair Linkage (# reads) Reference Length AMR Gene Family Drug Class Resistance Mechanism +mdtF 3000796 protein homolog model CARD 1 100.0 no data no data Escherichia coli 2.00 0.00 2.00 8.09 252.00 193.00 0 0 0 0 N/A N/A 3114 resistance-nodulation-cell division (RND) antibiotic efflux pump macrolide antibiotic; fluoroquinolone antibiotic; penam antibiotic efflux +mgrA 3000815 protein homolog model CARD 1 100.0 no data no data Staphylococcus aureus 1.00 0.00 1.00 19.59 87.00 172.00 0 0 0 0 N/A N/A 444 ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics antibiotic efflux +OprN 3000805 protein homolog model CARD 1 100.0 no data no data Pseudomonas aeruginosa 2.00 0.00 2.00 17.76 252.00 193.00 0 0 0 0 N/A N/A 1419 resistance-nodulation-cell division (RND) antibiotic efflux pump fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic antibiotic efflux +mepA 3000026 protein homolog model CARD 1 100.0 no data no data Staphylococcus aureus 2.00 0.00 2.00 17.70 240.00 190.50 0 0 0 0 N/A N/A 1356 multidrug and toxic compound extrusion (MATE) transporter glycylcycline; tetracycline antibiotic antibiotic efflux diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json new file mode 100644 index 0000000..6eaea2b --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json @@ -0,0 +1 @@ +{"k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630": {"ORF": "k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630", "contig": "k141_1617_82", "HSP": "gnl|BL_ORD_ID|4713|hsp_num:0", "ARO_model": "Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin", "type_hit": "Perfect", "#_of_kmers_in_sequence": 3501, "#_of_AMR_kmers": 2274, "taxonomic_info": {"species": {"Bifidobacterium longum": 75, "Bifidobacterium dentium": 67, "Parascardovia denticolens": 3, "Bifidobacterium animalis": 7, "Bifidobacterium bifidum": 9}, "genus": {}}, "genomic_info": {"chr + plasmid": 0, "plasmid": 0, "chr": 234}}} diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt new file mode 100644 index 0000000..4118b12 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt @@ -0,0 +1,2 @@ +ORF_ID Contig Cut_Off Best_Hit_ARO CARD*kmer Prediction Taxonomic kmers Genomic kmers +"NC_000962.3_273 # 314309 # 314854 # -1 # ID=1_273;partial=00;start_type=GTG;rbs_motif=AGG;rbs_spacer=4bp;gc_cont=0.679" NC_000962.3_273 Perfect AAC(2')-Ic Mycobacterium tuberculosis (chromosome) "Mycobacterium tuberculosis: 486; " "chr + plasmid: 0; plasmid: 0; chr: 486; " diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json new file mode 100644 index 0000000..6eaea2b --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis.json @@ -0,0 +1 @@ +{"k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630": {"ORF": "k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630", "contig": "k141_1617_82", "HSP": "gnl|BL_ORD_ID|4713|hsp_num:0", "ARO_model": "Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin", "type_hit": "Perfect", "#_of_kmers_in_sequence": 3501, "#_of_AMR_kmers": 2274, "taxonomic_info": {"species": {"Bifidobacterium longum": 75, "Bifidobacterium dentium": 67, "Parascardovia denticolens": 3, "Bifidobacterium animalis": 7, "Bifidobacterium bifidum": 9}, "genus": {}}, "genomic_info": {"chr + plasmid": 0, "plasmid": 0, "chr": 234}}} diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt new file mode 100644 index 0000000..4118b12 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_2/sample2/bin2/61mer_analysis_rgi_summary.txt @@ -0,0 +1,2 @@ +ORF_ID Contig Cut_Off Best_Hit_ARO CARD*kmer Prediction Taxonomic kmers Genomic kmers +"NC_000962.3_273 # 314309 # 314854 # -1 # ID=1_273;partial=00;start_type=GTG;rbs_motif=AGG;rbs_spacer=4bp;gc_cont=0.679" NC_000962.3_273 Perfect AAC(2')-Ic Mycobacterium tuberculosis (chromosome) "Mycobacterium tuberculosis: 486; " "chr + plasmid: 0; plasmid: 0; chr: 486; " diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt new file mode 100644 index 0000000..7eee60c --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.allele.txt @@ -0,0 +1,3 @@ +Reference Sequence Mapped reads with kmer DB hits CARD*kmer Prediction Single species (chromosome) reads Single species (chromosome or plasmid) reads Single species (plasmid) reads Single species (no genomic info) reads Single genus (chromosome) reads Single genus (chromosome or plasmid) reads Single genus (plasmid) reads Single genus (no genomic info) reads Promiscuous plasmid reads Unknown taxonomy (chromosome) reads Unknown taxonomy (chromosome or plasmid) reads Unknown taxonomy (no genomic info) reads +ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1 2 0 1 1 0 +ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1 2 0 2 0 0 diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json new file mode 100644 index 0000000..25108c6 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_1/sample1/61mer_analysis.json @@ -0,0 +1 @@ +{"NC_000913.3_208_0/1/1": {"reference": "ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1", "#_of_kmers_in_sequence": 66, "#_of_AMR_kmers": 66, "SAM_flag": 83, "MAPQ": 193, "taxonomic_info": {"species": {}, "genus": {}}, "genomic_info": {"chr + plasmid": 18, "plasmid": 0, "chr": 48}}} diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt new file mode 100644 index 0000000..7eee60c --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.allele.txt @@ -0,0 +1,3 @@ +Reference Sequence Mapped reads with kmer DB hits CARD*kmer Prediction Single species (chromosome) reads Single species (chromosome or plasmid) reads Single species (plasmid) reads Single species (no genomic info) reads Single genus (chromosome) reads Single genus (chromosome or plasmid) reads Single genus (plasmid) reads Single genus (no genomic info) reads Promiscuous plasmid reads Unknown taxonomy (chromosome) reads Unknown taxonomy (chromosome or plasmid) reads Unknown taxonomy (no genomic info) reads +ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1 2 0 1 1 0 +ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1 2 0 2 0 0 diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json new file mode 100644 index 0000000..25108c6 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_allele_2/sample2/61mer_analysis.json @@ -0,0 +1 @@ +{"NC_000913.3_208_0/1/1": {"reference": "ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1", "#_of_kmers_in_sequence": 66, "#_of_AMR_kmers": 66, "SAM_flag": 83, "MAPQ": 193, "taxonomic_info": {"species": {}, "genus": {}}, "genomic_info": {"chr + plasmid": 18, "plasmid": 0, "chr": 48}}} diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt new file mode 100644 index 0000000..e5912f1 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.gene.txt @@ -0,0 +1,3 @@ +ARO term Mapped reads with kmer DB hits CARD*kmer Prediction Single species (chromosome) reads Single species (chromosome or plasmid) reads Single species (plasmid) reads Single species (no genomic info) reads Single genus (chromosome) reads Single genus (chromosome or plasmid) reads Single genus (plasmid) reads Single genus (no genomic info) reads Promiscuous plasmid reads Unknown taxonomy (chromosome) reads Unknown taxonomy (chromosome or plasmid) reads Unknown taxonomy (no genomic info) reads +mdtP 2 0 1 1 0 +mdtF 2 0 2 0 0 diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json new file mode 100644 index 0000000..25108c6 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_1/sample1/61mer_analysis.json @@ -0,0 +1 @@ +{"NC_000913.3_208_0/1/1": {"reference": "ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1", "#_of_kmers_in_sequence": 66, "#_of_AMR_kmers": 66, "SAM_flag": 83, "MAPQ": 193, "taxonomic_info": {"species": {}, "genus": {}}, "genomic_info": {"chr + plasmid": 18, "plasmid": 0, "chr": 48}}} diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt new file mode 100644 index 0000000..e5912f1 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.gene.txt @@ -0,0 +1,3 @@ +ARO term Mapped reads with kmer DB hits CARD*kmer Prediction Single species (chromosome) reads Single species (chromosome or plasmid) reads Single species (plasmid) reads Single species (no genomic info) reads Single genus (chromosome) reads Single genus (chromosome or plasmid) reads Single genus (plasmid) reads Single genus (no genomic info) reads Promiscuous plasmid reads Unknown taxonomy (chromosome) reads Unknown taxonomy (chromosome or plasmid) reads Unknown taxonomy (no genomic info) reads +mdtP 2 0 1 1 0 +mdtF 2 0 2 0 0 diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json new file mode 100644 index 0000000..25108c6 --- /dev/null +++ b/q2_amr/card/tests/data/partitioned/kmer_analysis_reads_gene_2/sample2/61mer_analysis.json @@ -0,0 +1 @@ +{"NC_000913.3_208_0/1/1": {"reference": "ARO:3003550|ID:45|Name:mdtP|NCBI:AP009048.1", "#_of_kmers_in_sequence": 66, "#_of_AMR_kmers": 66, "SAM_flag": 83, "MAPQ": 193, "taxonomic_info": {"species": {}, "genus": {}}, "genomic_info": {"chr + plasmid": 18, "plasmid": 0, "chr": 48}}} diff --git a/q2_amr/card/tests/test_partition.py b/q2_amr/card/tests/test_partition.py index bdbf639..a700460 100644 --- a/q2_amr/card/tests/test_partition.py +++ b/q2_amr/card/tests/test_partition.py @@ -4,6 +4,12 @@ from qiime2.plugin.testing import TestPluginBase from q2_amr.card.partition import ( + collate_mags_annotations, + collate_mags_kmer_analyses, + collate_reads_allele_annotations, + collate_reads_allele_kmer_analyses, + collate_reads_gene_annotations, + collate_reads_gene_kmer_analyses, partition_mags_annotations, partition_reads_allele_annotations, partition_reads_gene_annotations, @@ -12,12 +18,148 @@ CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, CARDGeneAnnotationDirectoryFormat, + CARDMAGsKmerAnalysisDirectoryFormat, + CARDReadsAlleleKmerAnalysisDirectoryFormat, + CARDReadsGeneKmerAnalysisDirectoryFormat, ) class TestPartition(TestPluginBase): package = "q2_amr.card.tests" + def test_collate_mags_annotations(self): + # Test collate for mags annotations + self._test_collate( + data_dir="annotate_mags_output", + files_to_assert=["amr_annotation.json", "amr_annotation.txt"], + samples=["sample1/bin1", "sample2/bin2"], + format=CARDAnnotationDirectoryFormat, + function=collate_mags_annotations, + ) + + def test_collate_reads_allele_annotations(self): + # Test collate for reads allele annotations + self._test_collate( + data_dir="annotate_reads_allele_output", + files_to_assert=[ + "allele_mapping_data.txt", + "overall_mapping_stats.txt", + "sorted.length_100.bam", + ], + samples=["sample1", "sample2"], + format=CARDAlleleAnnotationDirectoryFormat, + function=collate_reads_allele_annotations, + ) + + def test_collate_reads_gene_annotations(self): + # Test collate for reads gene annotations + self._test_collate( + data_dir="annotate_reads_gene_output", + files_to_assert=["gene_mapping_data.txt"], + samples=["sample1", "sample2"], + format=CARDGeneAnnotationDirectoryFormat, + function=collate_reads_gene_annotations, + ) + + def test_collate_mags_kmer_analysis(self): + # Test collate for MAGs k-mer analysis + self._test_collate( + data_dir="kmer_analysis_mags", + files_to_assert=["61mer_analysis.json", "61mer_analysis_rgi_summary.txt"], + samples=["sample1/bin1", "sample2/bin2"], + format=CARDMAGsKmerAnalysisDirectoryFormat, + function=collate_mags_kmer_analyses, + ) + + def test_collate_reads_allele_kmer_analysis(self): + # Test collate for MAGs k-mer analysis + self._test_collate( + data_dir="kmer_analysis_reads_allele", + files_to_assert=["61mer_analysis.json", "61mer_analysis.allele.txt"], + samples=["sample1", "sample2"], + format=CARDReadsAlleleKmerAnalysisDirectoryFormat, + function=collate_reads_allele_kmer_analyses, + ) + + def test_collate_reads_gene_kmer_analysis(self): + # Test collate for MAGs k-mer analysis + self._test_collate( + data_dir="kmer_analysis_reads_gene", + files_to_assert=["61mer_analysis.json", "61mer_analysis.gene.txt"], + samples=["sample1", "sample2"], + format=CARDReadsGeneKmerAnalysisDirectoryFormat, + function=collate_reads_gene_kmer_analyses, + ) + + def _test_collate(self, data_dir, files_to_assert, samples, format, function): + # Set up the list with annotations objects to collate + artifact_1 = self.setup_annotations( + dir_name=f"partitioned/{data_dir}_1", format=format + ) + artifact_2 = self.setup_annotations( + dir_name=f"partitioned/{data_dir}_2", format=format + ) + + artifacts = [artifact_1, artifact_2] + + # Run collate functions on the annotations + collate = function(artifacts) + + # Assert if collated artifact has the correct format + self.assertTrue(isinstance(collate, format)) + + # Assert if all the files have been moved to the collated object + for sample in samples: + for file in files_to_assert: + self.assertTrue( + os.path.exists(os.path.join(collate.path, sample, file)) + ) + + def test_mags_file_exists_error(self): + # Set up the list with duplicated artifacts + artifact = self.setup_annotations( + dir_name="partitioned/kmer_analysis_reads_allele_1", + format=CARDReadsAlleleKmerAnalysisDirectoryFormat, + ) + + artifacts = [artifact, artifact] + + pattern = ( + r"The directory already exists: .*/sample1. Sample IDs must be " + r"unique across all artifacts. Each artifact in the list must be " + r"unique and cannot be repeated." + ) + + # Check if error is raised + with self.assertRaisesRegex(FileExistsError, pattern): + collate_reads_allele_kmer_analyses(artifacts) + + def test_reads_file_exists_error(self): + # Set up the list with duplicated artifacts + artifact = self.setup_annotations( + dir_name="partitioned/annotate_mags_output_1", + format=CARDAnnotationDirectoryFormat, + ) + + artifacts = [artifact, artifact] + + pattern = ( + r"The directory already exists: .*/bin1. MAG IDs must be " + r"unique across all artifacts. Each artifact in the list must be " + r"unique and cannot be repeated." + ) + + # Check if error is raised + with self.assertRaisesRegex(FileExistsError, pattern): + collate_reads_allele_kmer_analyses(artifacts) + + def setup_annotations(self, dir_name, format): + # Setup of the directory with dummy files and the needed directory format + annotations = format() + files = self.get_data_path(dir_name) + shutil.copytree(files, annotations.path, dirs_exist_ok=True) + return annotations + def test_partition_mags_annotations(self): # Set up for annotations annotations = self.setup_annotations( @@ -54,13 +196,6 @@ def test_partition_mags_warning_message(self): ): partition_mags_annotations(annotations=annotations, num_partitions=5) - def setup_annotations(self, dir_name, format): - # Setup of the directory with annotations files and the needed directory format - annotations = format() - files = self.get_data_path(dir_name) - shutil.copytree(files, annotations.path, dirs_exist_ok=True) - return annotations - def test_partition_reads_allele_annotations(self): self._test_partition_reads_annotations( dir="collated/annotate_reads_allele_output", diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py index 20ebbe8..b34fe2b 100644 --- a/q2_amr/plugin_setup.py +++ b/q2_amr/plugin_setup.py @@ -19,6 +19,7 @@ Choices, Collection, Int, + List, Properties, Range, Str, @@ -31,6 +32,12 @@ from q2_amr.card.heatmap import heatmap from q2_amr.card.mags import annotate_mags_card from q2_amr.card.partition import ( + collate_mags_annotations, + collate_mags_kmer_analyses, + collate_reads_allele_annotations, + collate_reads_allele_kmer_analyses, + collate_reads_gene_annotations, + collate_reads_gene_kmer_analyses, partition_mags_annotations, partition_reads_allele_annotations, partition_reads_gene_annotations, @@ -239,6 +246,113 @@ citations=[citations["alcock_card_2023"]], ) +plugin.methods.register_function( + function=collate_mags_annotations, + inputs={"annotations": List[SampleData[CARDAnnotation]]}, + parameters={}, + outputs={"collated_annotations": SampleData[CARDAnnotation]}, + input_descriptions={ + "annotations": "A collection of annotations from MAGs to be " "collated." + }, + name="Collate mags annotations.", + description="Takes a collection of SampleData[CARDAnnotation] " + "and collates them into a single artifact.", +) + +T_allele_annotation_collate_in, T_allele_annotation_collate_out = TypeMap( + { + SampleData[ + CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa") + ]: SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa")], + SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2")]: SampleData[ + CARDAlleleAnnotation % Properties("kma", "bowtie2") + ], + SampleData[CARDAlleleAnnotation % Properties("kma", "bwa")]: SampleData[ + CARDAlleleAnnotation % Properties("kma", "bwa") + ], + SampleData[CARDAlleleAnnotation % Properties("bowtie2", "bwa")]: SampleData[ + CARDAlleleAnnotation % Properties("bowtie2", "bwa") + ], + SampleData[CARDAlleleAnnotation % Properties("kma")]: SampleData[ + CARDAlleleAnnotation % Properties("kma") + ], + SampleData[CARDAlleleAnnotation % Properties("bowtie2")]: SampleData[ + CARDAlleleAnnotation % Properties("bowtie2") + ], + SampleData[CARDAlleleAnnotation % Properties("bwa")]: SampleData[ + CARDAlleleAnnotation % Properties("bwa") + ], + } +) + +plugin.methods.register_function( + function=collate_reads_allele_annotations, + inputs={"annotations": List[T_allele_annotation_collate_in]}, + parameters={}, + outputs={"collated_annotations": T_allele_annotation_collate_out}, + input_descriptions={ + "annotations": "A collection of annotations from reads at " + "allele level to be collated." + }, + name="Collate reads allele annotations.", + description="Takes a collection of SampleData[CARDAlleleAnnotation] " + "and collates them into a single artifact.", +) + +plugin.methods.register_function( + function=collate_reads_gene_annotations, + inputs={"annotations": List[SampleData[CARDGeneAnnotation]]}, + parameters={}, + outputs={"collated_annotations": SampleData[CARDGeneAnnotation]}, + input_descriptions={ + "annotations": "A collection of annotations from reads at " + "gene level to be collated." + }, + name="Collate reads gene annotations.", + description="Takes a collection of SampleData[CARDGeneAnnotation] " + "and collates them into a single artifact.", +) + +plugin.methods.register_function( + function=collate_mags_kmer_analyses, + inputs={"kmer_analyses": List[SampleData[CARDMAGsKmerAnalysis]]}, + parameters={}, + outputs={"collated_kmer_analyses": SampleData[CARDMAGsKmerAnalysis]}, + input_descriptions={ + "kmer_analyses": "A collection of k-mer analyses from MAG annotations." + }, + name="Collate k-mer analyses from MAG annotations.", + description="Takes a collection of SampleData[CARDMAGsKmerAnalysis] " + "and collates them into a single artifact.", +) + +plugin.methods.register_function( + function=collate_reads_allele_kmer_analyses, + inputs={"kmer_analyses": List[SampleData[CARDReadsAlleleKmerAnalysis]]}, + parameters={}, + outputs={"collated_kmer_analyses": SampleData[CARDReadsAlleleKmerAnalysis]}, + input_descriptions={ + "kmer_analyses": "A collection of k-mer analyses from reads annotations at " + "allele level." + }, + name="Collate k-mer analyses from reads annotations at allele level.", + description="Takes a collection of SampleData[CARDReadsAlleleKmerAnalysis] " + "and collates them into a single artifact.", +) + +plugin.methods.register_function( + function=collate_reads_gene_kmer_analyses, + inputs={"kmer_analyses": List[SampleData[CARDReadsGeneKmerAnalysis]]}, + parameters={}, + outputs={"collated_kmer_analyses": SampleData[CARDReadsGeneKmerAnalysis]}, + input_descriptions={ + "kmer_analyses": "A collection of k-mer analyses from reads annotations at " + "gene level." + }, + name="Collate k-mer analyses from reads annotations at gene level.", + description="Takes a collection of SampleData[CARDReadsGeneKmerAnalysis] " + "and collates them into a single artifact.", +) plugin.methods.register_function( function=partition_mags_annotations, inputs={"annotations": SampleData[CARDAnnotation]},