vanX gene in vanA cluster

Accession ARO:3002949
Synonym(s)vanXA vanX-A
CARD Short NamevanX_in_vanA_cl
DefinitionAlso known as vanXA, is a vanX variant found in the vanA gene cluster.
AMR Gene Familyglycopeptide resistance gene cluster, vanX
Drug Classglycopeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Perfect MatchesEnterococcus faecalisp+wgs, Enterococcus faeciump+wgs, Klebsiella pneumoniaewgs, Staphylococcus aureusp+wgs, Streptococcus gallolyticuswgs
Resistomes with Sequence VariantsBrevibacillus laterosporusg+wgs+gi, Enterococcus aviump, Enterococcus faecalisp+wgs, Enterococcus faeciumg+p+wgs, Klebsiella pneumoniaewgs, Staphylococcus aureusg+p+wgs, Streptococcus gallolyticuswgs
Classification13 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ vanX [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 vanX gene in vanA cluster among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 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 GI
Brevibacillus laterosporus16.67%0%17.65%100%
Enterococcus avium0%33.33%0%0%
Enterococcus faecalis0%2.71%6.24%0%
Enterococcus faecium0.96%10.75%28.74%0%
Klebsiella pneumoniae0%0%0.01%0%
Staphylococcus aureus0.7%0.19%0.13%0%
Streptococcus gallolyticus0%0%2.27%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): 200


>gb|AAA65957.1|+|vanX gene in vanA cluster [Enterococcus faecium]
MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNL
TKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSL
EWWHYVLRDEPYPNSYFDFPVK


>gb|M97297.1|+|8016-8624|vanX gene in vanA cluster [Enterococcus faecium]
ATGGAAATAGGATTTACTTTTTTAGATGAAATAGTACACGGTGTTCGTTGGGACGCTAAATATGCCACTTGGGATAATTTCACCGGAAAA
CCGGTTGACGGTTATGAAGTAAATCGCATTGTAGGGACATACGAGTTGGCTGAATCGCTTTTGAAGGCAAAAGAACTGGCTGCTACCCAA
GGGTACGGATTGCTTCTATGGGACGGTTACCGTCCTAAGCGTGCTGTAAACTGTTTTATGCAATGGGCTGCACAGCCGGAAAATAACCTG
ACAAAGGAAAGTTATTATCCCAATATTGACCGAACTGAGATGATTTCAAAAGGATACGTGGCTTCAAAATCAAGCCATAGCCGCGGCAGT
GCCATTGATCTTACGCTTTATCGATTAGACACGGGTGAGCTTGTACCAATGGGGAGCCGATTTGATTTTATGGATGAACGCTCTCATCAT
GCGGCAAATGGAATATCATGCAATGAAGCGCAAAATCGCAGACGTTTGCGCTCCATCATGGAAAACAGTGGGTTTGAAGCATATAGCCTC
GAATGGTGGCACTATGTATTAAGAGACGAACCATACCCCAATAGCTATTTTGATTTCCCCGTTAAATAA