vanY gene in vanF cluster

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Accession ARO:3002958
Synonym(s)vanY-F vanYF
CARD Short NamevanY_in_vanF_cl
DefinitionAlso known as vanYF, is a vanY variant found in the vanF gene cluster.
AMR Gene Familyglycopeptide resistance gene cluster, vanY
Drug Classglycopeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsBacillus amyloliquefacienswgs, Bacillus anthracisg+wgs, Bacillus cereusg+p+wgs, Bacillus pumiluswgs, Bacillus subtiliswgs, Bacillus thuringiensisg+p+wgs, Bacillus velezensiswgs, Blautia productag+wgs, Brevibacillus brevisg+wgs, Brevibacillus laterosporusg+wgs, Clostridium botulinumg+wgs, Clostridium sporogenesg, Erysipelatoclostridium ramosumg+wgs, Faecalibacterium prausnitziig+wgs, Kocuria palustriswgs, Lactococcus garvieaewgs, Macrococcus caniswgs, Micrococcus luteusg+wgs, Pseudomonas fluorescensp, Rothia mucilaginosag+wgs, Staphylococcus aureuswgs, Staphylococcus epidermidiswgs, Staphylococcus massiliensiswgs, Staphylococcus pasteurig+wgs, Staphylococcus warnerig+wgs, Streptococcus agalactiaewgs, Streptococcus iniaeg+wgs, Streptococcus intermediuswgs, Streptococcus pyogeneswgs, Streptococcus sobrinusg+wgs, Streptococcus uberisg+wgs
Classification12 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ vanY [AMR Gene Family]
+ part_of glycopeptide resistance gene cluster VanF
Publications

Fraimow H, et al. 2005. Antimicrob Agents Chemother 49(7): 2625-2633. Putative VanRS-like two-component regulatory system associated with the inducible glycopeptide resistance cluster of Paenibacillus popilliae. (PMID 15980329)
Resistomes

Prevalence of vanY gene in vanF 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 anthracis100%0%99.56%0%0%
Bacillus cereus89.25%2.13%88.63%0%0%
Bacillus pumilus0%0%1.12%0%0%
Bacillus subtilis0%0%0.29%0%0%
Bacillus thuringiensis55%0.07%61.78%0%0%
Bacillus velezensis0%0%0.37%0%0%
Blautia producta33.33%0%36.36%0%0%
Brevibacillus brevis85.71%0%50%0%0%
Brevibacillus laterosporus83.33%0%97.06%0%0%
Clostridium botulinum23.88%0%18.75%0%0%
Clostridium sporogenes8.33%0%0%0%0%
Erysipelatoclostridium ramosum100%0%100%0%0%
Faecalibacterium prausnitzii26.67%0%12.62%0%0%
Kocuria palustris0%0%94.44%0%0%
Lactococcus garvieae0%0%6.67%0%0%
Macrococcus canis0%0%50%0%0%
Micrococcus luteus22.22%0%3.33%0%0%
Pseudomonas fluorescens0%11.11%0%0%0%
Rothia mucilaginosa20%0%15.79%0%0%
Staphylococcus aureus0%0%0.01%0%0%
Staphylococcus epidermidis0%0%0.42%0%0%
Staphylococcus massiliensis0%0%85.71%0%0%
Staphylococcus pasteuri87.5%0%96.15%0%0%
Staphylococcus warneri83.33%0%87.7%0%0%
Streptococcus agalactiae0%0%0.06%0%0%
Streptococcus iniae100%0%98.84%0%0%
Streptococcus intermedius0%0%2.27%0%0%
Streptococcus pyogenes0%0%0.1%0%0%
Streptococcus sobrinus100%0%97.96%0%0%
Streptococcus uberis25%0%0.89%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|AAF36805.1|+|vanY gene in vanF cluster [Paenibacillus popilliae ATCC 14706]
MKKWGLLLVFALFLVFIFNILPISQDKVEDRIYEQNDKDTSDDKMTAENMQKIELTEEQIYQGNLLLVNNEHPVHQKSIKSDIINLFTHK
ELTKGYGLLDNEIKLSEEIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPAGHSEHNLGLSLDVGSTQMKMDKAPE
GKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYLDYLKEEKSISVRVDGKKYTISYDPISQNETIEVE
VPADEQYEISGNNIDGVIVTTFS


>gb|AF155139.1|+|3397-4278|vanY gene in vanF cluster [Paenibacillus popilliae ATCC 14706]
ATGAAAAAGTGGGGACTTTTATTGGTTTTTGCATTATTTCTAGTATTTATTTTTAATATATTACCGATATCCCAAGATAAAGTAGAGGAT
CGAATATATGAACAAAATGACAAAGATACATCGGATGATAAAATGACAGCTGAAAATATGCAAAAGATTGAGCTTACGGAAGAGCAGATC
TATCAAGGGAATCTACTCTTGGTCAACAATGAACATCCTGTTCACCAAAAGAGTATAAAATCGGATATTATAAATTTATTTACGCACAAA
GAATTGACAAAGGGGTATGGGTTACTTGATAACGAAATTAAATTGTCAGAGGAAATAGCTGGGAAATTTTCAGAGATGATAGCTGCGGCT
GAAGAGGATGGCGTTAGTAATTTTTTAATTAGCAGTGGTTATCGAGACTTGGATGAGCAAAGCAGACTTTATGAGGAAATGGGTTCTGAT
TTTGCTTTGCCAGCAGGTCATAGTGAACACAACTTGGGGTTATCGCTTGATGTAGGATCTACTCAAATGAAGATGGATAAAGCGCCTGAA
GGAAAGTGGATAGAAAAAAATTGTTGGGAATACGGCTTTATATTACGCTATCCCTTGGATAAAACGGATGTTACAGGAATTCAATATGAA
CCTTGGCATATTCGCTATGTCGGTTTGCCTCACAGTGCGATTATGCAGGAAATGAATTTAGCTTTGGAAGAATATTTAGATTATTTAAAA
GAAGAAAAGAGCATTTCTGTTCGTGTTGATGGGAAAAAATATACAATTTCATATGATCCCATTTCTCAAAACGAGACAATTGAAGTTGAA
GTACCAGCGGATGAACAGTATGAAATATCTGGTAATAATATTGATGGAGTAATTGTGACCACATTTTCTTGA

Curator Acknowledgements
Curator Description Most Recent Edit