From 75d4efa8dd33e7d8b17ea6e1c8c6dbe0e1fbd0b1 Mon Sep 17 00:00:00 2001 From: VinzentRisch <100149044+VinzentRisch@users.noreply.github.com> Date: Mon, 13 May 2024 16:18:42 +0200 Subject: [PATCH] ENH: add actions that can partition annotation artifacts from reads and MAGs (#54) Co-authored-by: Michal Ziemski --- q2_amr/card/partition.py | 93 +++++++ .../sample1/allele_mapping_data.txt | 5 + .../sample1/overall_mapping_stats.txt | 17 ++ .../sample1/sorted.length_100.bam | Bin 0 -> 564 bytes .../sample2/allele_mapping_data.txt | 5 + .../sample2/overall_mapping_stats.txt | 17 ++ .../sample2/sorted.length_100.bam | Bin 0 -> 564 bytes .../amr_annotation.json | 1 + .../amr_annotation.txt | 3 + .../amr_annotation.json | 1 + .../amr_annotation.txt | 3 + .../amr_annotation.json | 1 + .../amr_annotation.txt | 3 + .../sample1/gene_mapping_data.txt | 5 + .../sample2/gene_mapping_data.txt | 5 + q2_amr/card/tests/test_partition.py | 240 +++++++++++++++--- q2_amr/card/tests/test_utils.py | 35 ++- q2_amr/card/utils.py | 24 ++ q2_amr/plugin_setup.py | 120 ++++++++- .../bin1/61mer_analysis_rgi_summary.txt | 2 + 20 files changed, 540 insertions(+), 40 deletions(-) create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt create mode 100644 q2_amr/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json create mode 100644 q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt create mode 100644 q2_amr/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt create mode 100644 q2_amr/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt create mode 100644 q2_amr/types/tests/data/card_kmer_analysis_mags/sample1/bin1/61mer_analysis_rgi_summary.txt diff --git a/q2_amr/card/partition.py b/q2_amr/card/partition.py index 7031e69..50e4479 100644 --- a/q2_amr/card/partition.py +++ b/q2_amr/card/partition.py @@ -1,7 +1,11 @@ import os +import warnings +from typing import Union +import numpy as np from qiime2.util import duplicate +from q2_amr.card.utils import copy_files from q2_amr.types import ( CARDAlleleAnnotationDirectoryFormat, CARDAnnotationDirectoryFormat, @@ -98,3 +102,92 @@ def _collate(partition_list): duplicate(file, collated_partitions.path / sample.name / file.name) return collated_partitions + + +def partition_mags_annotations( + annotations: CARDAnnotationDirectoryFormat, num_partitions: int = None +) -> CARDAnnotationDirectoryFormat: + return _partition_annotations(annotations, num_partitions) + + +def partition_reads_allele_annotations( + annotations: CARDAlleleAnnotationDirectoryFormat, num_partitions: int = None +) -> CARDAlleleAnnotationDirectoryFormat: + return _partition_annotations(annotations, num_partitions) + + +def partition_reads_gene_annotations( + annotations: CARDGeneAnnotationDirectoryFormat, num_partitions: int = None +) -> CARDGeneAnnotationDirectoryFormat: + return _partition_annotations(annotations, num_partitions) + + +def _partition_annotations( + annotations: Union[ + CARDAnnotationDirectoryFormat, + CARDGeneAnnotationDirectoryFormat, + CARDAlleleAnnotationDirectoryFormat, + ], + num_partitions: int = None, +): + partitioned_annotations = {} + annotations_all = [] + # Add one tuples with sample ID, MAG ID and full paths to annotation files to + # annotations_all + if isinstance(annotations, CARDAnnotationDirectoryFormat): + for sample_id, mag in annotations.sample_dict().items(): + for mag_id, file_paths in mag.items(): + annotations_all.append((sample_id, mag_id, file_paths)) + + else: + for sample_id, file_paths in annotations.sample_dict().items(): + annotations_all.append((sample_id, file_paths)) + + # Sort annotations_all for consistent splitting behaviour + annotations_all.sort() + + # Retrieve the number of annotations + num_annotations = len(annotations_all) + + # If no number of partitions is specified or the number is higher than the number + # of annotations, all annotations get partitioned by annotation + if num_partitions is None: + num_partitions = num_annotations + elif num_partitions > num_annotations: + warnings.warn( + "You have requested a number of partitions" + f" '{num_partitions}' that is greater than your number" + f" of annotations '{num_annotations}'. Your data will be" + f" partitioned by annotation into '{num_annotations}'" + " partitions." + ) + num_partitions = num_annotations + + # Splits annotations into the specified number of arrays + arrays = np.array_split(np.array(annotations_all, dtype=object), num_partitions) + + for i, annotation_tuple in enumerate(arrays, 1): + # Creates directory with same format as input + partitioned_annotation = type(annotations)() + + # Constructs paths to all annotation files and moves them to the new partition + # directories + if isinstance(annotations, CARDAnnotationDirectoryFormat): + for sample_id, mag_id, file_paths in annotation_tuple: + copy_files(file_paths, partitioned_annotation.path, sample_id, mag_id) + + else: + mag_id = None + for sample_id, file_paths in annotation_tuple: + copy_files(file_paths, partitioned_annotation.path, sample_id) + + # Set key for partitioned_annotations dict to mag_id or sample_id + partitioned_annotation_key = mag_id if mag_id else sample_id + + # Add the partitioned object to the collection dict + if num_partitions == num_annotations: + partitioned_annotations[partitioned_annotation_key] = partitioned_annotation + else: + partitioned_annotations[i] = partitioned_annotation + + return partitioned_annotations diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt b/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/allele_mapping_data.txt new file mode 100644 index 0000000..8add729 --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_allele_annotation/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/collated/card_allele_annotation/sample1/overall_mapping_stats.txt b/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/overall_mapping_stats.txt new file mode 100644 index 0000000..60e7d3b --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_allele_annotation/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/collated/card_allele_annotation/sample1/sorted.length_100.bam b/q2_amr/card/tests/data/collated/card_allele_annotation/sample1/sorted.length_100.bam new file mode 100644 index 0000000000000000000000000000000000000000..9b257a6036a2dbe8b269d86aeba5fa1bf02935ce GIT binary patch literal 564 zcmb2|=3rp}f&Xj_PR>jW{ft{D-}XD?AkcPQLjP6p8}1T*-HzG%?`UcNxUfc{d4&c$FXz3pXKOzH|9>VXZcATWKjVtH>vMlk2o$lHYvw)W(o2o! zVROQ)&HdC<#JA@@6D|@9*;Bdr9Fx;anUqkvpHGV{H6q`uq1en+zHzGSy5$@H&+*&vaMKBvqggrK8(qUrFiGl7mwRdX z>DpGsUBPn$Z>?MTS}x>nQiI3B)&ClIZILUk{9%)vbaO72Ey$C%^xDu$xWDg`;);!rX<^%P#$me_8mvc4>K<;10Q&DHaDy zr}iv8vG$yG&w^Vouywp2fbHQdt_}m^Fg9(dosoZUCJmq8h ra>=f&Z?>i>oabKeT6%l)n@@`$aDTlcko*Uj9MIh%&A<#!CLjU;D@Xj7 literal 0 HcmV?d00001 diff --git a/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt b/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/allele_mapping_data.txt new file mode 100644 index 0000000..8add729 --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_allele_annotation/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/collated/card_allele_annotation/sample2/overall_mapping_stats.txt b/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/overall_mapping_stats.txt new file mode 100644 index 0000000..60e7d3b --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_allele_annotation/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/collated/card_allele_annotation/sample2/sorted.length_100.bam b/q2_amr/card/tests/data/collated/card_allele_annotation/sample2/sorted.length_100.bam new file mode 100644 index 0000000000000000000000000000000000000000..9b257a6036a2dbe8b269d86aeba5fa1bf02935ce GIT binary patch literal 564 zcmb2|=3rp}f&Xj_PR>jW{ft{D-}XD?AkcPQLjP6p8}1T*-HzG%?`UcNxUfc{d4&c$FXz3pXKOzH|9>VXZcATWKjVtH>vMlk2o$lHYvw)W(o2o! zVROQ)&HdC<#JA@@6D|@9*;Bdr9Fx;anUqkvpHGV{H6q`uq1en+zHzGSy5$@H&+*&vaMKBvqggrK8(qUrFiGl7mwRdX z>DpGsUBPn$Z>?MTS}x>nQiI3B)&ClIZILUk{9%)vbaO72Ey$C%^xDu$xWDg`;);!rX<^%P#$me_8mvc4>K<;10Q&DHaDy zr}iv8vG$yG&w^Vouywp2fbHQdt_}m^Fg9(dosoZUCJmq8h ra>=f&Z?>i>oabKeT6%l)n@@`$aDTlcko*Uj9MIh%&A<#!CLjU;D@Xj7 literal 0 HcmV?d00001 diff --git a/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json b/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.json new file mode 100644 index 0000000..d49ca4d --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/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/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt b/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.txt new file mode 100644 index 0000000..1f16da6 --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/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/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json b/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.json new file mode 100644 index 0000000..d49ca4d --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/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/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt b/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.txt new file mode 100644 index 0000000..dbf3c40 --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/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/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json b/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.json new file mode 100644 index 0000000..d49ca4d --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/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/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt b/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/amr_annotation.txt new file mode 100644 index 0000000..dbf3c40 --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/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/collated/card_gene_annotation/sample1/gene_mapping_data.txt b/q2_amr/card/tests/data/collated/card_gene_annotation/sample1/gene_mapping_data.txt new file mode 100644 index 0000000..873522c --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_gene_annotation/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/collated/card_gene_annotation/sample2/gene_mapping_data.txt b/q2_amr/card/tests/data/collated/card_gene_annotation/sample2/gene_mapping_data.txt new file mode 100644 index 0000000..873522c --- /dev/null +++ b/q2_amr/card/tests/data/collated/card_gene_annotation/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/test_partition.py b/q2_amr/card/tests/test_partition.py index e9c948c..b6e9b7d 100644 --- a/q2_amr/card/tests/test_partition.py +++ b/q2_amr/card/tests/test_partition.py @@ -1,5 +1,4 @@ import os -import shutil from qiime2.plugin.testing import TestPluginBase @@ -10,6 +9,9 @@ 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, ) from q2_amr.types import ( CARDAlleleAnnotationDirectoryFormat, @@ -27,83 +29,92 @@ class TestPartition(TestPluginBase): def test_collate_mags_annotations(self): # Test collate for mags annotations self._test_collate( - data_dir="annotate_mags_output", + data_dir="partitioned/annotate_mags_output", files_to_assert=["amr_annotation.json", "amr_annotation.txt"], samples=["sample1/bin1", "sample2/bin2"], - format=CARDAnnotationDirectoryFormat, + dir_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", + data_dir="partitioned/annotate_reads_allele_output", files_to_assert=[ "allele_mapping_data.txt", "overall_mapping_stats.txt", "sorted.length_100.bam", ], samples=["sample1", "sample2"], - format=CARDAlleleAnnotationDirectoryFormat, + dir_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", + data_dir="partitioned/annotate_reads_gene_output", files_to_assert=["gene_mapping_data.txt"], samples=["sample1", "sample2"], - format=CARDGeneAnnotationDirectoryFormat, + dir_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", + data_dir="partitioned/kmer_analysis_mags", files_to_assert=["61mer_analysis.json", "61mer_analysis_rgi_summary.txt"], samples=["sample1/bin1", "sample2/bin2"], - format=CARDMAGsKmerAnalysisDirectoryFormat, + dir_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", + data_dir="partitioned/kmer_analysis_reads_allele", files_to_assert=["61mer_analysis.json", "61mer_analysis.allele.txt"], samples=["sample1", "sample2"], - format=CARDReadsAlleleKmerAnalysisDirectoryFormat, + dir_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", + data_dir="partitioned/kmer_analysis_reads_gene", files_to_assert=["61mer_analysis.json", "61mer_analysis.gene.txt"], samples=["sample1", "sample2"], - format=CARDReadsGeneKmerAnalysisDirectoryFormat, + dir_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 - ) + def _test_collate(self, data_dir, files_to_assert, samples, dir_format, function): + """ + This function is used to test collation functions. A list with two artifacts + is created that is used as input for the collate function. Assertions are made + if all expected annotation files are in the collated directory. + Args: + data_dir: Name of package data directory with the test files. + files_to_assert (list): A list of filenames that have to be present in + the collated directory. + samples (list): A list of sample names used to construct the file paths + to the files listed in files_to_assert. + dir_format: Name of QIIME2 directory format. + function: Collate function that should be tested. + """ + # Set up the list with annotations objects to collate + artifact_1 = dir_format(path=self.get_data_path(f"{data_dir}_1"), mode="r") + artifact_2 = dir_format(path=self.get_data_path(f"{data_dir}_2"), mode="r") 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)) + self.assertTrue(isinstance(collate, dir_format)) # Assert if all the files have been moved to the collated object for sample in samples: @@ -114,11 +125,8 @@ def _test_collate(self, data_dir, files_to_assert, samples, format, function): 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, - ) - + path = self.get_data_path("partitioned/kmer_analysis_reads_allele_1") + artifact = CARDReadsAlleleKmerAnalysisDirectoryFormat(path=path, mode="r") artifacts = [artifact, artifact] pattern = ( @@ -133,11 +141,8 @@ def test_mags_file_exists_error(self): 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, - ) - + path = self.get_data_path("partitioned/annotate_mags_output_1") + artifact = CARDAnnotationDirectoryFormat(path=path, mode="r") artifacts = [artifact, artifact] pattern = ( @@ -150,9 +155,168 @@ def test_reads_file_exists_error(self): 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 + path = self.get_data_path("collated/card_annotation") + annotations = CARDAnnotationDirectoryFormat(path=path, mode="r") + + # Run partition_mags_annotations + obs = partition_mags_annotations(annotations=annotations, num_partitions=3) + + mag_ids = [ + "e026af61-d911-4de3-a957-7e8bf837f30d", + "aa447c99-ecd9-4c4a-a53b-4df6999815dd", + "f5a16381-ea80-49f9-875e-620f333a9293", + ] + + # Assert if keys of collection are correct + self.assertTrue(set(obs.keys()) == set(mag_ids)) + + # Assert if all files exist in the correct locations + paths = [ + os.path.join( + obs["e026af61-d911-4de3-a957-7e8bf837f30d"].path, + "sample1", + "e026af61-d911-4de3-a957-7e8bf837f30d", + "amr_annotation.txt", + ), + os.path.join( + obs["e026af61-d911-4de3-a957-7e8bf837f30d"].path, + "sample1", + "e026af61-d911-4de3-a957-7e8bf837f30d", + "amr_annotation.json", + ), + os.path.join( + obs["aa447c99-ecd9-4c4a-a53b-4df6999815dd"].path, + "sample2", + "aa447c99-ecd9-4c4a-a53b-4df6999815dd", + "amr_annotation.txt", + ), + os.path.join( + obs["aa447c99-ecd9-4c4a-a53b-4df6999815dd"].path, + "sample2", + "aa447c99-ecd9-4c4a-a53b-4df6999815dd", + "amr_annotation.json", + ), + os.path.join( + obs["f5a16381-ea80-49f9-875e-620f333a9293"].path, + "sample2", + "f5a16381-ea80-49f9-875e-620f333a9293", + "amr_annotation.json", + ), + os.path.join( + obs["f5a16381-ea80-49f9-875e-620f333a9293"].path, + "sample2", + "f5a16381-ea80-49f9-875e-620f333a9293", + "amr_annotation.txt", + ), + ] + for path in paths: + self.assertTrue(os.path.exists(path)) + + def test_partition_mags_annotations_uneven(self): + # Set up for annotations + path = self.get_data_path("collated/card_annotation") + annotations = CARDAnnotationDirectoryFormat(path=path, mode="r") + + # Run partition_mags_annotations + obs = partition_mags_annotations(annotations=annotations, num_partitions=2) + + # Assert if keys of collection are correct + self.assertTrue(set(obs.keys()) == {1, 2}) + + # Assert if all files exist in the correct locations + paths = [ + os.path.join( + obs[1].path, + "sample1", + "e026af61-d911-4de3-a957-7e8bf837f30d", + "amr_annotation.txt", + ), + os.path.join( + obs[1].path, + "sample1", + "e026af61-d911-4de3-a957-7e8bf837f30d", + "amr_annotation.json", + ), + os.path.join( + obs[1].path, + "sample2", + "aa447c99-ecd9-4c4a-a53b-4df6999815dd", + "amr_annotation.txt", + ), + os.path.join( + obs[1].path, + "sample2", + "aa447c99-ecd9-4c4a-a53b-4df6999815dd", + "amr_annotation.json", + ), + os.path.join( + obs[2].path, + "sample2", + "f5a16381-ea80-49f9-875e-620f333a9293", + "amr_annotation.json", + ), + os.path.join( + obs[2].path, + "sample2", + "f5a16381-ea80-49f9-875e-620f333a9293", + "amr_annotation.txt", + ), + ] + for path in paths: + self.assertTrue(os.path.exists(path)) + + def test_partition_mags_warning_message(self): + # Test warning message when partitioning MAG annotations with num partitions + # higher than the number of annotations + path = self.get_data_path("collated/card_annotation") + annotations = CARDAnnotationDirectoryFormat(path=path, mode="r") + + with self.assertWarnsRegex( + UserWarning, "You have requested a number of.*5.*3.*3" + ): + partition_mags_annotations(annotations=annotations, num_partitions=5) + + def test_partition_reads_gene_annotations(self): + # Set up for annotations + path = self.get_data_path("collated/card_gene_annotation") + annotations = CARDGeneAnnotationDirectoryFormat(path=path, mode="r") + + # Run function + obs = partition_reads_gene_annotations(annotations=annotations) + + # Assert if keys of collection are correct + self.assertTrue(set(obs.keys()) == {"sample2", "sample1"}) + + file_paths = [ + os.path.join(obs["sample1"].path, "sample1", "gene_mapping_data.txt"), + os.path.join(obs["sample2"].path, "sample2", "gene_mapping_data.txt"), + ] + # Assert if all files exist in the right location + for file_path in file_paths: + self.assertTrue(os.path.exists(file_path)) + + def test_partition_reads_allele_annotations(self): + # Set up for annotations + path = self.get_data_path("collated/card_allele_annotation") + annotations = CARDAlleleAnnotationDirectoryFormat(path=path, mode="r") + + # Run function + obs = partition_reads_allele_annotations(annotations=annotations) + + # Assert if keys of collection are correct + self.assertTrue(set(obs.keys()) == {"sample2", "sample1"}) + + file_paths = [ + os.path.join(obs["sample1"].path, "sample1", "allele_mapping_data.txt"), + os.path.join(obs["sample1"].path, "sample1", "overall_mapping_stats.txt"), + os.path.join(obs["sample1"].path, "sample1", "sorted.length_100.bam"), + os.path.join(obs["sample2"].path, "sample2", "allele_mapping_data.txt"), + os.path.join(obs["sample2"].path, "sample2", "overall_mapping_stats.txt"), + os.path.join(obs["sample2"].path, "sample2", "sorted.length_100.bam"), + ] + + # Assert if all files exist in the right location + for file_path in file_paths: + self.assertTrue(os.path.exists(file_path)) diff --git a/q2_amr/card/tests/test_utils.py b/q2_amr/card/tests/test_utils.py index d9229d3..9b8a23b 100644 --- a/q2_amr/card/tests/test_utils.py +++ b/q2_amr/card/tests/test_utils.py @@ -6,7 +6,13 @@ import pandas as pd from qiime2.plugin.testing import TestPluginBase -from q2_amr.card.utils import colorify, create_count_table, load_card_db, read_in_txt +from q2_amr.card.utils import ( + colorify, + copy_files, + create_count_table, + load_card_db, + read_in_txt, +) from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat @@ -198,3 +204,30 @@ def test_colorify(self): colored_string = colorify(string) expected_output = "\033[1;32mHello, world!\033[0m" self.assertEqual(colored_string, expected_output) + + def test_copy_files(self): + # Setup test files + self.tmp = self.temp_dir.name + + file_path_1 = os.path.join(self.tmp, "DNA_fasta.fasta") + file_path_2 = os.path.join(self.tmp, "DNA_fasta_-.fasta") + + shutil.copy(self.get_data_path("DNA_fasta.fasta"), self.tmp) + shutil.copy(self.get_data_path("DNA_fasta_-.fasta"), self.tmp) + + # Call the function + file_paths = [file_path_1, file_path_2] + dst_path_components = [self.tmp, "dst_folder_1", "dst_folder_2"] + + copy_files(file_paths, *dst_path_components) + + # Assert if both files have been copied to the correct location + dst_path_1 = os.path.join( + self.tmp, "dst_folder_1", "dst_folder_2", "DNA_fasta.fasta" + ) + dst_path_2 = os.path.join( + self.tmp, "dst_folder_1", "dst_folder_2", "DNA_fasta_-.fasta" + ) + + self.assertTrue(os.path.exists(dst_path_1)) + self.assertTrue(os.path.exists(dst_path_2)) diff --git a/q2_amr/card/utils.py b/q2_amr/card/utils.py index af8bd76..e460ad4 100644 --- a/q2_amr/card/utils.py +++ b/q2_amr/card/utils.py @@ -5,6 +5,7 @@ from functools import reduce import pandas as pd +from qiime2.util import duplicate EXTERNAL_CMD_WARNING = ( "Running external command line application(s). " @@ -138,3 +139,26 @@ def create_count_table(df_list: list) -> pd.DataFrame: def colorify(string: str): return "%s%s%s" % ("\033[1;32m", string, "\033[0m") + + +def copy_files(file_paths: list, *dst_path_components): + """ + Creates a destination file path out of the *dst_path_components. Then creates + the directory for the destination file path if it doesn't exist already and + finally copies the file from source path to destination path. + + Args: + file_paths (list): A list of source file paths to be copied. + *dst_path_components: Variable number of arguments representing destination + path components that will be joined together to form the destination file + path. + """ + for src in file_paths: + # Construct destination file path with destination file path components + dst = os.path.join(*dst_path_components, os.path.basename(src)) + + # Create destination directory if it not already exists + os.makedirs(os.path.dirname(dst), exist_ok=True) + + # Copy file from source to destination + duplicate(src, dst) diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py index fe4481c..bc8fdb9 100644 --- a/q2_amr/plugin_setup.py +++ b/q2_amr/plugin_setup.py @@ -14,7 +14,17 @@ SequencesWithQuality, ) from q2_types.sample_data import SampleData -from qiime2.core.type import Bool, Choices, Int, List, Properties, Range, Str, TypeMap +from qiime2.core.type import ( + Bool, + Choices, + Collection, + Int, + List, + Properties, + Range, + Str, + TypeMap, +) from qiime2.plugin import Citations, Plugin from q2_amr import __version__ @@ -28,6 +38,9 @@ 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, ) from q2_amr.card.reads import annotate_reads_card from q2_amr.types import ( @@ -340,6 +353,111 @@ 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]}, + parameters={"num_partitions": Int % Range(1, None)}, + outputs={"partitioned_annotations": Collection[SampleData[CARDAnnotation]]}, + input_descriptions={"annotations": "The annotations to partition."}, + parameter_descriptions={ + "num_partitions": "The number of partitions to split the annotations " + "into. Defaults to partitioning into individual annotations." + }, + output_descriptions={"partitioned_annotations": "partitioned annotations"}, + name="Partition annotations", + description="Partition amr annotations of MAGs into a collections of individual " + "artifacts or the number of partitions specified.", +) + +T_allele_annotation_in, T_allele_annotation_out = TypeMap( + { + SampleData[ + CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa") + ]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa")] + ], + SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2")] + ], + SampleData[CARDAlleleAnnotation % Properties("kma", "bwa")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("kma", "bwa")] + ], + SampleData[CARDAlleleAnnotation % Properties("bowtie2", "bwa")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("bowtie2", "bwa")] + ], + SampleData[CARDAlleleAnnotation % Properties("kma")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("kma")] + ], + SampleData[CARDAlleleAnnotation % Properties("bowtie2")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("bowtie2")] + ], + SampleData[CARDAlleleAnnotation % Properties("bwa")]: Collection[ + SampleData[CARDAlleleAnnotation % Properties("bwa")] + ], + } +) + +plugin.methods.register_function( + function=partition_reads_allele_annotations, + inputs={"annotations": T_allele_annotation_in}, + parameters={"num_partitions": Int % Range(1, None)}, + outputs={"partitioned_annotations": T_allele_annotation_out}, + input_descriptions={"annotations": "The annotations to partition."}, + parameter_descriptions={ + "num_partitions": "The number of partitions to split the annotations " + "into. Defaults to partitioning into individual annotations." + }, + output_descriptions={"partitioned_annotations": "partitioned annotations"}, + name="Partition annotations", + description="Partition amr annotations of reads at allele level into a collections " + "of individual artifacts or the number of partitions specified.", +) + +T_gene_annotation_in, T_gene_annotation_out = TypeMap( + { + SampleData[ + CARDGeneAnnotation % Properties("kma", "bowtie2", "bwa") + ]: Collection[ + SampleData[CARDGeneAnnotation % Properties("kma", "bowtie2", "bwa")] + ], + SampleData[CARDGeneAnnotation % Properties("kma", "bowtie2")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("kma", "bowtie2")] + ], + SampleData[CARDGeneAnnotation % Properties("kma", "bwa")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("kma", "bwa")] + ], + SampleData[CARDGeneAnnotation % Properties("bowtie2", "bwa")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("bowtie2", "bwa")] + ], + SampleData[CARDGeneAnnotation % Properties("kma")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("kma")] + ], + SampleData[CARDGeneAnnotation % Properties("bowtie2")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("bowtie2")] + ], + SampleData[CARDGeneAnnotation % Properties("bwa")]: Collection[ + SampleData[CARDGeneAnnotation % Properties("bwa")] + ], + } +) + +plugin.methods.register_function( + function=partition_reads_gene_annotations, + inputs={"annotations": T_gene_annotation_in}, + parameters={"num_partitions": Int % Range(1, None)}, + outputs={"partitioned_annotations": T_gene_annotation_out}, + input_descriptions={"annotations": "The annotations to partition."}, + parameter_descriptions={ + "num_partitions": "The number of partitions to split the annotations" + " into. Defaults to partitioning into individual annotations." + }, + output_descriptions={"partitioned_annotations": "partitioned annotations"}, + name="Partition annotations", + description="Partition amr annotations of reads at gene level into a collection of" + " individual artifacts or the number of partitions specified.", +) + + # Registrations plugin.register_semantic_types( CARDDatabase, diff --git a/q2_amr/types/tests/data/card_kmer_analysis_mags/sample1/bin1/61mer_analysis_rgi_summary.txt b/q2_amr/types/tests/data/card_kmer_analysis_mags/sample1/bin1/61mer_analysis_rgi_summary.txt new file mode 100644 index 0000000..4118b12 --- /dev/null +++ b/q2_amr/types/tests/data/card_kmer_analysis_mags/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; "