rpsJ

Accession ARO:3003930
Synonym(s)nusE
DefinitionrpsJ is a tetracycline resistance protein identified in Neisseria gonorrhoeae. Tetracycline resistance is conferred by binding to the ribosome as a 30S ribosomal protection protein.
AMR Gene Familytetracycline-resistant ribosomal protection protein
Drug Classtetracycline antibiotic
Resistance Mechanismantibiotic target protection
Classification8 ontology terms | Show
Parent Term(s)1 ontology terms | Show
Publications

Kubanov A, et al. 2016. BMC Infect. Dis. 16:389 Molecular epidemiology of drug-resistant Neisseria gonorrhoeae in Russia (Current Status, 2015). (PMID 27506605)

Resistomes

Prevalence of rpsJ among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for 82 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, 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 variant model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
Neisseria gonorrhoeae84.62%0%85.05%
Neisseria meningitidis0%0%8.61%
Show Perfect Only


Detection Models

Model Type: protein variant model

Model Definition: The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.

Legend:

  • discovered in clinical, agricultural, or environmental isolates
  • discovered via laboratory selection experiments


Bit-score Cut-off (blastP): 200

PMID: 27506605V57L V57M

>gb|AAW90462.1|-|rpsJ [Neisseria gonorrhoeae FA 1090]
MANQKIRIRLKAYDYALIDRSAQEIVETAKRTGAVVKGPIPLPTKIERFNILRSPHVNKT
SREQLEIRTHLRLMDIVDWTDKTTDALMKLDLPAGVDVEIKVQ



>gb|AE004969.1|-|1807359-1807670|rpsJ [Neisseria gonorrhoeae FA 1090]
ATGGCAAACCAAAAAATCCGTATCCGCCTGAAAGCTTATGATTACGCCCTGATTGACCGTTCTGCACAAGAAATCGTTGAAACTGCAAAA
CGTACCGGTGCTGTTGTAAAAGGCCCGATTCCTTTGCCGACCAAAATCGAGCGTTTCAACATTTTGCGTTCTCCGCACGTGAACAAAACT
TCCCGTGAACAATTGGAAATCCGCACCCATTTGCGCCTGATGGACATCGTGGATTGGACCGATAAAACTACCGATGCGCTGATGAAGCTG
GATTTGCCGGCCGGTGTTGATGTAGAAATTAAAGTCCAATAA