PmrF

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Ontology CARD's Antibiotic Resistance Ontology
Accession ARO:3003578
Synonym(s)arnC
CARD Short NamePmrF
DefinitionPmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A, which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.
AMR Gene Familypmr phosphoethanolamine transferase
Drug Classpeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Perfect MatchesEscherichia colig+p+wgs, Shigella boydiig+wgs, Shigella dysenteriaeg, Shigella flexnerig+wgs, Shigella sonneig+wgs
Resistomes with Sequence VariantsCitrobacter amalonaticusg+wgs, Citrobacter freundiig+p+wgs, Citrobacter portucalensisg+wgs, Citrobacter werkmaniig+wgs, Citrobacter youngaeg+wgs, Enterobacter cloacaewgs, Enterobacter hormaecheig+wgs, Escherichia albertiig+wgs, Escherichia colig+p+wgs, Escherichia fergusoniig+wgs, Escherichia marmotaeg+wgs, Salmonella bongorig+wgs, Salmonella entericag+wgs, Shigella boydiig+wgs, Shigella dysenteriaeg+wgs, Shigella flexnerig+wgs, Shigella sonneig+wgs
Classification12 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic polymyxin B [Antibiotic]
+ pmr phosphoethanolamine transferase [AMR Gene Family]
Sub-Term(s)
2 ontology terms | Show
+ cprRS regulates
+ basRS regulates
Publications

Gunn JS, et al. 1998. Mol Microbiol 27(6): 1171-1182. PmrA-PmrB-regulated genes necessary for 4-aminoarabinose lipid A modification and polymyxin resistance. (PMID 9570402)
Resistomes

Prevalence of PmrF 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
Citrobacter amalonaticus100%0%100%0%0%
Citrobacter freundii99.18%0.31%98.45%0%0%
Citrobacter portucalensis100%0%100%0%0%
Citrobacter werkmanii100%0%100%0%0%
Citrobacter youngae100%0%100%0%0%
Enterobacter cloacae0%0%0.96%0%0%
Enterobacter hormaechei11.87%0%12.17%0%0%
Escherichia albertii98.57%0%97.42%0%0%
Escherichia coli67.48%0.04%98.59%0%99.11%
Escherichia fergusonii100%0%97.83%0%0%
Escherichia marmotae100%0%97.92%0%0%
Salmonella bongori91.67%0%100%0%0%
Salmonella enterica94.7%0%98.14%0%0%
Shigella boydii60%0%62.22%0%0%
Shigella dysenteriae28.57%0%60%0%0%
Shigella flexneri99%0%97.67%0%0%
Shigella sonnei100%0%94.96%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): 550


>gb|AAC75314.1|+|PmrF [Escherichia coli str. K-12 substr. MG1655]
MFEIHPVKKVSVVIPVYNEQESLPELIRRTTTACESLGKEYEILLIDDGSSDNSAHMLVEASQAENSHIVSILLNRNYGQHSAIMAGFSH
VTGDLIITLDADLQNPPEEIPRLVAKADEGYDVVGTVRQNRQDSWFRKTASKMINRLIQRTTGKAMGDYGCMLRAYRRHIVDAMLHCHER
STFIPILANIFARRAIEIPVHHAEREFGESKYSFMRLINLMYDLVTCLTTTPLRMLSLLGSIIAIGGFSIAVLLVILRLTFGPQWAAEGV
FMLFAVLFTFIGAQFIGMGLLGEYIGRIYTDVRARPRYFVQQVIRPSSKENE


>gb|U00096.1|+|2367071-2368039|PmrF [Escherichia coli str. K-12 substr. MG1655]
ATGTTTGAAATCCACCCTGTTAAGAAAGTCTCGGTGGTTATTCCCGTTTATAACGAGCAGGAAAGCTTACCGGAATTAATCAGGCGCACC
ACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCGATAATTCCGCGCATATGCTGGTCGAA
GCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCAC
GTTACTGGCGACTTAATTATTACCCTTGATGCCGATCTCCAGAATCCGCCAGAAGAAATCCCCCGCCTGGTGGCAAAAGCCGATGAAGGT
TACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGC
ACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACGC
AGCACCTTTATCCCGATTCTGGCGAATATCTTCGCCCGCCGTGCCATTGAAATTCCAGTACATCATGCCGAGCGTGAGTTTGGTGAATCC
AAATACAGTTTTATGCGCCTGATTAATTTGATGTACGACCTGGTGACCTGCCTTACCACAACGCCGCTACGTATGCTGAGTCTGCTCGGC
AGCATTATTGCGATTGGAGGTTTTAGCATTGCGGTGCTGCTGGTGATTTTACGCCTGACCTTCGGACCACAATGGGCGGCAGAAGGCGTC
TTTATGCTATTTGCCGTGCTGTTTACTTTTATTGGCGCTCAGTTTATCGGCATGGGATTACTCGGTGAATATATCGGCAGGATCTACACC
GATGTCCGCGCCCGCCCCCGCTATTTTGTTCAGCAAGTTATCCGTCCATCCAGCAAGGAAAATGAATAA

Curator Acknowledgements
Curator Description Most Recent Edit