LpxC

Accession ARO:3003574
DefinitionThe LpxC gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane
AMR Gene FamilyAcinetobacter mutant Lpx gene conferring resistance to colistin
Drug Classpeptide antibiotic
Resistance Mechanismantibiotic target alteration
Classification16 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic colistin A [Antibiotic]
+ confers_resistance_to_antibiotic colistin B [Antibiotic]
+ Acinetobacter mutant Lpx gene conferring resistance to colistin [AMR Gene Family]
Publications

Moffatt JH, et al. 2010. Antimicrob Agents Chemother 54(12): 4971-4977. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. (PMID 20855724)

Beceiro A, et al. 2013. Antimicrob Agents Chemother 58(1): 518-526. Biological cost of different mechanisms of colistin resistance and their impact on virulence in Acinetobacter baumannii. (PMID 24189257)

Resistomes

Prevalence of LpxC 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

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
No prevalence data


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): 550


>gb|AJF83452.1|-|LpxC [Acinetobacter baumannii]
MVKQRTLNRVVKASGIGLHSGQKVMINFIPHTVDGGIVFRRIDLDPPVDIPANALLIQEA
FMCSNLVTGDIKVGTIEHVMSAIAGLGIDNLIVEVSASEVPIMDGSAGPFIYLLMQGGLR
EQDAPKKFIKILKPVEALIDDKKAIFSPHNGFQLNFTIDFDHPAFAKEYQSATIDFSTET
FVYEVSEARTFGFMKDLDYLKANNLALGASLDNAIGVDDTGVVNEEGLRFADEFVRHKIL
DAVGDLYLLGHQIIAKFDGYKSGHALNNQLLRNVQSDPSNYEIVTFDDEKDCPIPYVSVT



>gb|CP010781.1|-|3758032-3758934|LpxC [Acinetobacter baumannii]
ATGGTGAAACAGCGTACTCTCAATCGTGTGGTAAAAGCGAGTGGAATAGGTCTTCATAGCGGTCAAAAAGTGATGATCAATTTCATTCCA
CATACCGTGGATGGAGGTATTGTATTTCGCCGTATCGATTTGGATCCACCTGTCGATATTCCTGCTAATGCATTGCTGATTCAAGAAGCA
TTTATGTGTTCAAATCTTGTTACTGGCGATATTAAAGTCGGGACAATCGAACATGTGATGAGTGCGATTGCCGGTTTAGGAATCGATAAC
TTAATTGTGGAAGTGTCTGCTTCTGAAGTTCCAATTATGGATGGTAGTGCTGGTCCATTTATTTATTTGCTCATGCAAGGTGGCTTGCGT
GAACAAGATGCTCCTAAGAAATTTATAAAAATATTAAAGCCAGTTGAGGCTTTAATTGATGATAAAAAAGCAATATTCAGCCCGCATAAT
GGCTTTCAGCTTAACTTTACGATTGATTTTGATCATCCTGCATTTGCCAAAGAATATCAGTCTGCAACTATCGATTTTTCTACTGAAACG
TTTGTGTATGAGGTCAGTGAGGCACGAACTTTTGGTTTTATGAAAGACTTGGATTACCTTAAAGCAAATAATTTAGCTTTAGGAGCAAGT
CTAGATAATGCAATTGGCGTAGATGATACAGGTGTTGTAAACGAAGAAGGTTTACGATTTGCCGATGAGTTTGTTCGTCACAAAATTTTA
GATGCAGTTGGTGATTTGTATTTACTTGGTCATCAAATTATTGCCAAGTTTGATGGCTATAAATCAGGACATGCCTTAAATAATCAGCTA
TTACGCAATGTTCAAAGCGATCCGAGTAATTATGAAATTGTAACATTTGATGACGAGAAAGACTGTCCAATTCCATACGTGAGTGTGACA
TAA