vanY gene in vanM cluster

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Accession ARO:3002961
Synonym(s)vanY-M vanYM
CARD Short NamevanY_in_vanM_cl
DefinitionAlso known as vanYM, is a vanY variant found in the vanM gene cluster.
AMR Gene Familyglycopeptide resistance gene cluster, vanY
Drug Classglycopeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Perfect MatchesEnterococcus faeciumg+p+wgs+gi, Klebsiella pneumoniaewgs
Resistomes with Sequence VariantsBacillus amyloliquefacienswgs, Bacillus anthracisg+wgs, Bacillus cereusg+p+wgs, Bacillus pumilusg+wgs, Bacillus subtilisg+wgs, Bacillus thuringiensisg+p+wgs, Blautia productag+wgs, Borrelia crociduraeg, Borrelia recurrentisg, Borreliella afzeliig, Borreliella gariniig+wgs, Brachyspira pilosicoliwgs, Brevibacillus laterosporusg+wgs, Burkholderia multivoranswgs, Christensenella minutag+wgs, Clostridium botulinumg+wgs, Clostridium septicumg+wgs, Cutibacterium acneswgs, Enterococcus faeciumg+p+wgs+gi, Erysipelatoclostridium ramosumwgs, Faecalibacterium prausnitziig+wgs, Glutamicibacter creatinolyticusg, Klebsiella pneumoniaewgs, Klebsiella quasipneumoniaewgs, Kocuria palustriswgs, Leifsonia xylig+wgs, Listeria innocuag+wgs, Listeria monocytogenesg+p+wgs, Lysobacter oculig, Macrococcus canisg+wgs, Micrococcus luteusg+wgs, Paeniclostridium sordelliig+wgs, Parvimonas micrag+wgs, Pseudomonas syringaeg, Rothia mucilaginosag+wgs, Staphylococcus arlettaeg+wgs, Staphylococcus aureusg+wgs, Staphylococcus epidermidisg+wgs, Staphylococcus equorumg+p+wgs, Staphylococcus haemolyticusg+wgs, Staphylococcus pasteurig, Staphylococcus saprophyticusg+wgs, Staphylococcus simulansg+wgs, Staphylococcus warneriwgs, Stenotrophomonas maltophiliawgs, Streptococcus agalactiaeg+wgs, Streptococcus anginosusg+wgs, Streptococcus constellatusg+wgs, Streptococcus cristatusg+wgs, Streptococcus gordoniig+wgs, Streptococcus gwangjuenseg+wgs, Streptococcus intermediuswgs, Streptococcus mitisg+wgs, Streptococcus pneumoniaeg+wgs, Streptococcus pseudopneumoniaeg+wgs, Streptococcus pyogeneswgs, Streptococcus sanguinisg+wgs, Streptococcus suisg+wgs, Streptococcus urinalisg+wgs, Treponema denticolag+wgs, Treponema pallidumg+wgs, Xanthomonas campestrisg+wgs
Classification13 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ vanY [AMR Gene Family]
+ part_of glycopeptide resistance gene cluster VanM
Publications

Xu X, et al. 2010. Antimicrob Agents Chemother 54(11): 4643-4647. vanM, a new glycopeptide resistance gene cluster found in Enterococcus faecium. (PMID 20733041)
Resistomes

Prevalence of vanY gene in vanM 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)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
Bacillus amyloliquefaciens0%0%1.12%0%0%
Bacillus anthracis97.54%0%92.98%0%0%
Bacillus cereus72.04%1.82%91.33%0%0%
Bacillus pumilus15%0%1.12%0%0%
Bacillus subtilis64.52%0%66.76%0%0%
Bacillus thuringiensis91.25%0.39%97.73%0%0%
Blautia producta66.67%0%54.55%0%0%
Borrelia crocidurae100%0%0%0%0%
Borrelia recurrentis100%0%0%0%0%
Borreliella afzelii42.42%0%0%0%0%
Borreliella garinii9.86%0%25%0%0%
Brachyspira pilosicoli0%0%4.55%0%0%
Brevibacillus laterosporus50%0%76.47%0%0%
Burkholderia multivorans0%0%0.24%0%0%
Christensenella minuta100%0%100%0%0%
Clostridium botulinum1.49%0%0.82%0%0%
Clostridium septicum100%0%100%0%0%
Cutibacterium acnes0%0%0.26%0%0%
Enterococcus faecium0.96%0.26%0.51%1.96%0%
Erysipelatoclostridium ramosum0%0%1.16%0%0%
Escherichia coli0%0%0%0%0%
Faecalibacterium prausnitzii20%0%2.91%0%0%
Glutamicibacter creatinolyticus100%0%0%0%0%
Klebsiella pneumoniae0%0%0.15%0%0%
Klebsiella quasipneumoniae0%0%0.13%0%0%
Kocuria palustris0%0%5.56%0%0%
Leifsonia xyli100%0%100%0%0%
Listeria innocua5.88%0%7.52%0%0%
Listeria monocytogenes99.44%0.97%99.6%0%0%
Lysobacter oculi100%0%0%0%0%
Macrococcus canis78.57%0%62.5%0%0%
Micrococcus luteus61.11%0%72.22%0%0%
Paeniclostridium sordellii100%0%100%0%0%
Parvimonas micra30%0%43.75%0%0%
Pseudomonas syringae2.08%0%0%0%0%
Rothia mucilaginosa60%0%63.16%0%0%
Staphylococcus arlettae100%0%100%0%0%
Staphylococcus aureus3.49%0%0.24%0%0%
Staphylococcus epidermidis3.87%0%1.51%0%0%
Staphylococcus equorum100%2.7%91.07%0%0%
Staphylococcus haemolyticus51.72%0%57.8%0%0%
Staphylococcus pasteuri12.5%0%0%0%0%
Staphylococcus saprophyticus100%0%100%0%0%
Staphylococcus simulans100%0%96.61%0%0%
Staphylococcus warneri0%0%4.1%0%0%
Stenotrophomonas maltophilia0%0%0.74%0%0%
Streptococcus agalactiae2.8%0%0.26%0%0%
Streptococcus anginosus100%0%95.91%0%0%
Streptococcus constellatus100%0%95.45%0%0%
Streptococcus cristatus100%0%100%0%0%
Streptococcus gordonii100%0%98.72%0%0%
Streptococcus gwangjuense100%0%100%0%0%
Streptococcus intermedius0%0%4.55%0%0%
Streptococcus mitis100%0%98.99%0%0%
Streptococcus pneumoniae75.73%0%70.93%0%0%
Streptococcus pseudopneumoniae100%0%100%0%0%
Streptococcus pyogenes0%0%0.1%0%0%
Streptococcus sanguinis28.57%0%43.3%0%0%
Streptococcus suis12%0%8.34%0%0%
Streptococcus urinalis100%0%100%0%0%
Treponema denticola100%0%100%0%0%
Treponema pallidum100%0%88.89%0%0%
Xanthomonas campestris1.06%0%0.79%0%0%
Show Perfect Only


Detection Models

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


>gb|ACL82959.1|+|vanY gene in vanM cluster [Enterococcus faecium]
MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMG
SDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDF
LKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR


>gb|FJ349556.1|+|3057-3758|vanY gene in vanM cluster [Enterococcus faecium]
ATGGTCTTTCAAGGAAACTTACTCTTGGTTAATAACGAATATCCGGTTCTCGAAGAGAGTATAAAAACAGACGTTGTAAATTTATTTAAA
CATGATGAATTGACAAAAGGATATGAATTGCTCAATAGGGAAATTTATTTATCGGAGAAAGTTGCCCGTGAATTTTCAGAGATGGTAGAT
GCGGCTGAAAAAGAAGGAGTTCGCCATTTTTCAATCAATAGTGGGTTTCGAAACTTTGATGAGCAAAATGCCCTTTATCAAGAAATGGGG
TCTGACTACGCCTTGCCTGCAGGTTATAGCGAACATAATTTAGGTTTAGCACTTGATATCGGATCTACTCAAATGGAAATGAGTGAGGCA
CCGGAAGGAAAGTGGCTAGAAGATAATGCGTGGGAATACGGCTTTATTTTACGCTATCCAATGGACAAAACGGCCATCACAGGTATTCAG
TATGAACCTTGGCATTTTCGCTATGTGGGATTACCGCACAGTGCAATTATAGAGGAAAAGAATTTTGCTTTAGAAGAATATTTGGATTTC
CTAAAAGAACAAAAATCCATTTCAGGTACTATACATGGCGAAAATTATGAGATTTCTTATTATCCTATTACCGAAAAAACAGACATTGAA
ATGCCTGCCAATCTTCATTATGAAATATCAGGAAACAATATGGATGGTGTGATTGTGACAGTGTATCGCTAA

Curator Acknowledgements
Curator Description Most Recent Edit