vanY gene in vanA cluster

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Accession	ARO:3002955
Synonym(s)	vanY-A vanYA
CARD Short Name	vanY_in_vanA_cl
Definition	Also known as vanYA, is a vanY variant found in the vanA gene cluster.
AMR Gene Family	glycopeptide resistance gene cluster, vanY
Drug Class	glycopeptide antibiotic
Resistance Mechanism	antibiotic target alteration
Resistomes with Perfect Matches	Enterococcus faecalis^p+wgs, Enterococcus faecium^p+wgs, Klebsiella pneumoniae^wgs, Staphylococcus aureus^wgs
Resistomes with Sequence Variants	Bacillus anthracis^g+wgs, Bacillus cereus^g+p+wgs, Bacillus pumilus^wgs, Bacillus subtilis^wgs, Bacillus thuringiensis^g+p+wgs, Borreliella afzelii^g, Borreliella garinii^g+wgs, Brevibacillus brevis^g+wgs, Brevibacillus laterosporus^g+wgs+gi, Enterococcus avium^p, Enterococcus faecalis^p+wgs, Enterococcus faecium^g+p+wgs, Glutamicibacter creatinolyticus^g, Herbinix luporum^g+wgs, Klebsiella pneumoniae^wgs, Lactococcus garvieae^g+wgs, Leclercia adecarboxylata^wgs, Macrococcus canis^g+wgs, Micrococcus luteus^g+wgs, Paenibacillus mucilaginosus^wgs, Parvimonas micra^g+wgs, Pseudomonas putida^wgs, Pseudomonas stutzeri^wgs, Rhodopseudomonas palustris^g+wgs, Salmonella enterica^wgs, Staphylococcus aureus^g+p+wgs, Staphylococcus capitis^wgs, Staphylococcus epidermidis^wgs, Staphylococcus equorum^wgs, Staphylococcus haemolyticus^g+wgs, Staphylococcus simulans^wgs, Streptococcus agalactiae^wgs, Streptococcus constellatus^wgs, Streptococcus cristatus^wgs, Streptococcus gordonii^wgs, Streptococcus sanguinis^g+wgs, Streptococcus uberis^wgs, Treponema pallidum^wgs, Vibrio vulnificus^wgs
Classification	13 ontology terms \| Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + restructuring of bacterial cell wall conferring antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + glycopeptide antibiotic [Drug Class] + protein(s) conferring antibiotic resistance via molecular bypass + antibiotic resistance gene cluster, cassette, or operon + gene(s) or protein(s) associated with a glycopeptide resistance cluster + glycopeptide resistance gene cluster [AMR Gene Family] + teicoplanin [Antibiotic] + vancomycin [Antibiotic]
Parent Term(s)	2 ontology terms \| Show + vanY [AMR Gene Family] + part_of glycopeptide resistance gene cluster VanA
Publications	Courvalin P. 2005. Clin Infect Dis 42(SUPPL 1): S25-S34. Vancomycin resistance in gram-positive cocci. (PMID 16323116) Arthur M, et al. 1993. J Bacteriol 175(1): 117-127. Characterization of Tn1546, a Tn3-related transposon conferring glycopeptide resistance by synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. (PMID 8380148)

Resistomes

Prevalence of vanY gene in vanA cluster among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein homolog model (view sequences)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI	GRDI-AMR2
Bacillus anthracis	0%	0%	0%	0%	0%
Bacillus anthracis	100%	0%	100%	0%	0%
Bacillus cereus	0%	0%	0%	0%	0%
Bacillus cereus	66.67%	3.04%	45.16%	0%	0%
Bacillus pumilus	0%	0%	0%	0%	0%
Bacillus pumilus	0%	0%	0.56%	0%	0%
Bacillus subtilis	0%	0%	0.29%	0%	0%
Bacillus subtilis	0%	0%	0%	0%	0%
Bacillus thuringiensis	66.25%	1.31%	68.24%	0%	0%
Bacillus thuringiensis	0%	0%	0%	0%	0%
Borreliella afzelii	0%	0%	0%	0%	0%
Borreliella afzelii	57.58%	0%	0%	0%	0%
Borreliella garinii	0%	0%	0%	0%	0%
Borreliella garinii	90.14%	0%	75%	0%	0%
Brevibacillus brevis	0%	0%	0%	0%	0%
Brevibacillus brevis	100%	0%	100%	0%	0%
Brevibacillus laterosporus	0%	0%	0%	0%	0%
Brevibacillus laterosporus	83.33%	0%	82.35%	100%	0%
Enterococcus avium	0%	0%	0%	0%	0%
Enterococcus avium	0%	33.33%	0%	0%	0%
Enterococcus faecalis	0%	2.71%	8.04%	0%	0%
Enterococcus faecalis	0%	0.74%	4.55%	0%	0%
Enterococcus faecium	0%	4.73%	24.47%	0%	0%
Enterococcus faecium	0.96%	9.97%	47.71%	0%	0%
Escherichia coli	0%	0%	0%	0%	0%
Escherichia coli	0%	0%	0%	0%	0%
Glutamicibacter creatinolyticus	100%	0%	0%	0%	0%
Glutamicibacter creatinolyticus	0%	0%	0%	0%	0%
Herbinix luporum	100%	0%	100%	0%	0%
Herbinix luporum	0%	0%	0%	0%	0%
Klebsiella pneumoniae	0%	0%	0.02%	0%	0%
Klebsiella pneumoniae	0%	0%	0.01%	0%	0%
Lactococcus garvieae	5.56%	0%	4.44%	0%	0%
Lactococcus garvieae	0%	0%	0%	0%	0%
Leclercia adecarboxylata	0%	0%	2.33%	0%	0%
Leclercia adecarboxylata	0%	0%	0%	0%	0%
Macrococcus canis	0%	0%	0%	0%	0%
Macrococcus canis	100%	0%	100%	0%	0%
Micrococcus luteus	16.67%	0%	24.44%	0%	0%
Micrococcus luteus	0%	0%	0%	0%	0%
Paenibacillus mucilaginosus	0%	0%	0%	0%	0%
Paenibacillus mucilaginosus	0%	0%	50%	0%	0%
Parvimonas micra	0%	0%	0%	0%	0%
Parvimonas micra	30%	0%	37.5%	0%	0%
Pseudomonas putida	0%	0%	0%	0%	0%
Pseudomonas putida	0%	0%	0.53%	0%	0%
Pseudomonas stutzeri	0%	0%	0%	0%	0%
Pseudomonas stutzeri	0%	0%	0.76%	0%	0%
Rhodopseudomonas palustris	0%	0%	0%	0%	0%
Rhodopseudomonas palustris	7.69%	0%	11.11%	0%	0%
Salmonella enterica	0%	0%	0.01%	0%	0%
Salmonella enterica	0%	0%	0%	0%	0%
Staphylococcus aureus	0.7%	0.19%	0.13%	0%	0%
Staphylococcus aureus	0%	0%	0.01%	0%	0%
Staphylococcus capitis	0%	0%	0.63%	0%	0%
Staphylococcus capitis	0%	0%	0%	0%	0%
Staphylococcus epidermidis	0%	0%	0.5%	0%	0%
Staphylococcus epidermidis	0%	0%	0%	0%	0%
Staphylococcus equorum	0%	0%	0%	0%	0%
Staphylococcus equorum	0%	0%	5.36%	0%	0%
Staphylococcus haemolyticus	17.24%	0%	23.08%	0%	0%
Staphylococcus haemolyticus	0%	0%	0%	0%	0%
Staphylococcus simulans	0%	0%	0%	0%	0%
Staphylococcus simulans	0%	0%	3.39%	0%	0%
Streptococcus agalactiae	0%	0%	0%	0%	0%
Streptococcus agalactiae	0%	0%	0.13%	0%	0%
Streptococcus constellatus	0%	0%	0%	0%	0%
Streptococcus constellatus	0%	0%	4.55%	0%	0%
Streptococcus cristatus	0%	0%	2.86%	0%	0%
Streptococcus cristatus	0%	0%	0%	0%	0%
Streptococcus gordonii	0%	0%	1.28%	0%	0%
Streptococcus gordonii	0%	0%	0%	0%	0%
Streptococcus sanguinis	14.29%	0%	14.43%	0%	0%
Streptococcus sanguinis	0%	0%	0%	0%	0%
Streptococcus uberis	0%	0%	0.89%	0%	0%
Streptococcus uberis	0%	0%	0%	0%	0%
Treponema pallidum	0%	0%	11.11%	0%	0%
Treponema pallidum	0%	0%	0%	0%	0%
Vibrio vulnificus	0%	0%	0%	0%	0%
Vibrio vulnificus	0%	0%	0.41%	0%	0%

Show Perfect Only

Detection Models

protein homolog model

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 50

Protein
DNA

>gb|AAA65958.1|+|vanY gene in vanA cluster [Enterococcus faecium]
MKKLFFLLLLLFLIYLGYDYVNEALFSQEKVEFQNYDQNPKEHLENSGTSENTQEKTITEEQVYQGNLLLINSKYPVRQESVKSDIVNLS
KHDELINGYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLYQEMGAEYALPAGYSEHNSGLSLDVGSSLTKMER
APEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYMDYLKEEKTISVSVNGEKYEIFYYPVTKNTTI
HVPTNLRYEISGNNIDGVIVTVFPGSTHTNSRR

>gb|M97297.1|+|9052-9963|vanY gene in vanA cluster [Enterococcus faecium]
ATGAAGAAGTTGTTTTTTTTATTGTTATTGTTATTCTTAATATACTTAGGTTATGACTACGTTAATGAAGCACTGTTTTCTCAGGAAAAA
GTCGAATTTCAAAATTATGATCAAAATCCCAAAGAACATTTAGAAAATAGTGGGACTTCTGAAAATACCCAAGAGAAAACAATTACAGAA
GAACAGGTTTATCAAGGAAATCTGCTATTAATCAATAGTAAATATCCTGTTCGCCAAGAAAGTGTGAAGTCAGATATCGTGAATTTATCT
AAACATGACGAATTAATAAATGGATACGGGTTGCTTGATAGTAATATTTATATGTCAAAAGAAATAGCACAAAAATTTTCAGAGATGGTC
AATGATGCTGTAAAGGGTGGCGTTAGTCATTTTATTATTAATAGTGGCTATCGAGACTTTGATGAGCAAAGTGTGCTTTACCAAGAAATG
GGGGCTGAGTATGCCTTACCAGCAGGTTATAGTGAGCATAATTCAGGTTTATCACTAGATGTAGGATCAAGCTTGACGAAAATGGAACGA
GCCCCTGAAGGAAAGTGGATAGAAGAAAATGCTTGGAAATACGGGTTCATTTTACGTTATCCAGAGGACAAAACAGAGTTAACAGGAATT
CAATATGAACCATGGCATATTCGCTATGTTGGTTTACCACATAGTGCGATTATGAAAGAAAAGAATTTCGTTCTCGAGGAATATATGGAT
TACCTAAAAGAAGAAAAAACCATTTCTGTTAGTGTAAATGGGGAAAAATATGAGATCTTTTATTATCCTGTTACTAAAAATACCACCATT
CATGTGCCGACTAATCTTCGTTATGAGATATCAGGAAACAATATAGACGGTGTAATTGTGACAGTGTTTCCCGGATCAACACATACTAAT
TCAAGGAGGTAA

Curator Acknowledgements

Curator	Description	Most Recent Edit

vanY gene in vanA cluster

Prevalence: protein homolog model (view sequences)

Graph