OpmD

Accession ARO:3000809
Synonym(s)ompD
DefinitionOpmD is the outer membrane channel protein of the efflux complex MexGHI-OpmD.
AMR Gene Familyresistance-nodulation-cell division (RND) antibiotic efflux pump
Drug Classtetracycline antibiotic, fluoroquinolone antibiotic, phenicol antibiotic, diaminopyrimidine antibiotic, acridine dye, penam, aminocoumarin antibiotic, glycylcycline, macrolide antibiotic, triclosan, aminoglycoside antibiotic, monobactam, carbapenem, antibacterial free fatty acids
Resistance Mechanismantibiotic efflux
Efflux Componentefflux pump complex or subunit conferring antibiotic resistance
ResistomesPseudomonas fluorescensg
Classification26 ontology terms | Show
Parent Term(s)2 ontology terms | Show
Publications

Schweizer HP. 2003. Genet Mol Res 2(1): 48-62. Efflux as a mechanism of resistance to antimicrobials in Pseudomonas aeruginosa and related bacteria: unanswered questions. (PMID 12917802)

Aendekerk S, et al. 2005. Microbiology 151(PT 4): 1113-1125. The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication. (PMID 15817779)

Aendekerk S, et al. 2002. Microbiology (Reading, Engl.) 148(Pt 8):2371-81 Characterization of a new efflux pump, MexGHI-OpmD, from Pseudomonas aeruginosa that confers resistance to vanadium. (PMID 12177331)

Sekiya H, et al. 2003. Antimicrob. Agents Chemother. 47(9):2990-2 Functional cloning and characterization of a multidrug efflux pump, mexHI-opmD, from a Pseudomonas aeruginosa mutant. (PMID 12937010)

Resistomes

Prevalence of OpmD 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 homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
Enterobacter cloacae0%0%0%
Escherichia coli0%0%0%
Klebsiella pneumoniae0%0%0%
Morganella morganii0%0%0%
Mycobacterium tuberculosis0%0%0.03%
Pseudomonas aeruginosa0%0%0%
Pseudomonas fluorescens3.7%0%0%
Serratia marcescens0%0%0%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.

Bit-score Cut-off (blastP): 920


>gb|AAG07595.1|+|opmD [Pseudomonas aeruginosa PAO1]
MKRSYPNLSRLALALAVGTGLAACSVGPDYQRPQSPPPRVASEHLGEFSGERREAPWWSFFDDPQLVRLVDQALARNHDIREARANLRSA
RALFDDRWLDQLPQVTSQAGYSRSIEQQLDYDGEPRRRLAESYRAGFDAQWEIDLFGRLGRLSDAALARAEAADADLRLVRLSIAADTAR
AYFEIQGYQRRLDVARAQVRSWRDTLELTRSSLQLGSGLPEDVENAQANLLRSEAAIPPLTTALESARYRLDVLRGEAPGSGAPILDGGA
AAPLAKNLPLGDVDRLILQRPDVVSAERQLAASTEDVGAATAELYPRLDLGGFIGFFALRSGDLGSASRAFELAPSVSWPAFRLGNVRAR
LRAVEAQSDAALARYQRSLLLAQEDVGNALNQLAEHQRRLVALFQSATHGANALEIANERYRAGAGSYLAVLENQRALYQIREELAQAET
ASFVNVIALYKALGWGSGDLAPGAGQLAAGETAGANR


>gb|AE004091.2|+|4710621-4712084|opmD [Pseudomonas aeruginosa PAO1]
ATGAAGCGCTCCTACCCGAACCTTTCGCGCCTGGCGCTGGCCCTGGCGGTCGGCACCGGCCTGGCCGCCTGCAGCGTCGGCCCCGACTAC
CAGCGTCCGCAGTCGCCGCCGCCACGCGTCGCCAGCGAGCACCTCGGCGAGTTCTCCGGCGAGCGGCGGGAAGCGCCCTGGTGGAGTTTC
TTCGACGATCCGCAACTGGTGCGCCTGGTCGACCAGGCGCTGGCGCGCAACCACGACATCCGCGAGGCCCGCGCCAACCTGCGCAGCGCC
CGCGCGCTGTTCGACGACCGCTGGCTCGACCAGTTGCCGCAGGTCACCAGCCAGGCCGGCTACAGCCGCAGCATCGAACAACAGCTGGAC
TACGACGGCGAGCCGCGCCGGCGCCTGGCGGAGAGCTACCGCGCCGGCTTCGACGCGCAGTGGGAAATCGACCTGTTCGGCCGCCTCGGC
CGACTTTCCGACGCCGCCTTGGCCCGCGCCGAAGCGGCCGACGCCGACCTCCGGCTGGTACGCCTGAGCATCGCCGCCGACACCGCCCGC
GCCTACTTCGAGATCCAGGGCTACCAGCGCCGGCTGGACGTGGCGCGCGCCCAGGTGCGCAGTTGGCGCGACACCCTGGAGCTGACCCGC
AGCAGCCTGCAACTGGGCAGCGGCCTGCCGGAGGACGTGGAGAACGCCCAGGCCAACCTGCTGCGCAGCGAAGCGGCGATTCCGCCACTG
ACGACCGCGCTGGAGAGCGCCCGCTATCGCCTCGACGTGCTGCGCGGCGAGGCACCCGGCAGCGGCGCGCCGATCCTCGACGGCGGCGCC
GCCGCGCCATTGGCGAAGAACCTGCCGCTGGGCGACGTCGACCGCCTGATCCTCCAGCGCCCCGACGTAGTCAGCGCCGAGCGGCAACTG
GCAGCGAGCACCGAAGACGTCGGCGCGGCCACCGCCGAACTCTATCCGCGCCTCGACCTGGGCGGCTTCATCGGTTTCTTCGCCCTGCGC
AGCGGCGACCTCGGCAGCGCCTCGCGCGCCTTCGAACTGGCGCCCAGCGTCAGTTGGCCGGCGTTCCGCCTGGGCAACGTGCGGGCCCGC
CTGCGCGCCGTCGAGGCGCAGTCCGACGCCGCGCTGGCGCGCTACCAGCGCTCCCTGCTGCTGGCCCAGGAGGACGTCGGCAACGCGCTC
AACCAACTGGCCGAACACCAGCGTCGGCTGGTCGCCCTGTTCCAGTCCGCGACCCATGGCGCGAACGCCCTGGAGATCGCCAACGAACGC
TACCGCGCCGGCGCCGGCAGCTACCTGGCGGTGCTGGAGAACCAGCGCGCGCTGTACCAGATCCGCGAGGAACTGGCGCAGGCGGAGACC
GCCTCGTTCGTCAACGTCATCGCGCTCTACAAGGCGCTCGGCTGGGGCAGCGGCGACCTGGCGCCGGGCGCCGGCCAACTGGCCGCCGGC
GAAACCGCCGGGGCCAACCGTTGA