PEDO-3

Accession ARO:3003715
CARD Short NamePEDO-3
DefinitionPEDO-3 is a class B1 metallo-beta lactamase isolated from Pedobacter kyungheensis exhibiting resistance to carbapenems.
AMR Gene Familysubclass B1 PEDO beta-lactamase
Drug Classcarbapenem
Resistance Mechanismantibiotic inactivation
Classification13 ontology terms | Show
Parent Term(s)1 ontology terms | Show
Publications

Gudeta DD, et al. 2015. Antimicrob. Agents Chemother. : The Soil Microbiota Harbors a Diversity of Carbapenem-Hydrolyzing [beta]-Lactamases of Potential Clinical Relevance. (PMID 26482314)

Resistomes

Prevalence of PEDO-3 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

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


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): 400


>gb|AJP77076.1|-|PEDO-3 [Pedobacter sp. Stok-3]
MRYLLSFLLCLSAFASFAQNPKIKIKHLTGDLYVYTTYNTYKGALTDANAVYLVTNKGVVVIDAPWDATQFQPFLDSIQTKHHQKVVLAI
ATHSHGDRAGGLAFFKSKGIKTYTNKLTDEILKTNKEPRAAYTFTNDTTFTVGQYKINTYYAGKGHTKDNLVVWFPKDKVLFGGCLIKSI
EANDLGYIGESDLAAWPKSIEKLKQKYPDTKIVITGHAAWGNRESLDHTLKLLREKK


>gb|KP109679.1|-|2261-2974|PEDO-3 [Pedobacter sp. Stok-3]
ATGCGTTATCTTCTTTCCTTTTTACTTTGTTTATCTGCCTTTGCCTCTTTCGCGCAAAATCCAAAAATAAAAATCAAACATTTAACTGGC
GATCTTTATGTTTACACCACATACAATACCTACAAAGGCGCTTTAACAGATGCAAATGCGGTTTACCTGGTTACCAATAAAGGTGTTGTA
GTAATCGATGCCCCTTGGGATGCTACGCAGTTCCAGCCCTTTTTAGACTCTATTCAGACCAAACATCACCAAAAAGTAGTGCTGGCCATT
GCCACACATTCGCATGGCGACCGCGCAGGCGGTTTAGCGTTCTTTAAAAGTAAGGGCATAAAAACCTATACCAATAAATTAACCGACGAA
ATTCTGAAAACTAATAAAGAGCCACGCGCAGCCTACACCTTTACCAACGACACTACTTTTACAGTGGGACAATATAAAATAAACACCTAC
TATGCCGGCAAGGGGCATACAAAGGATAATCTGGTAGTTTGGTTTCCAAAAGACAAAGTTTTATTCGGTGGCTGCCTGATTAAAAGCATC
GAAGCCAATGATTTGGGCTATATTGGAGAATCCGATTTAGCCGCATGGCCAAAAAGCATCGAAAAGTTAAAACAGAAATATCCTGATACC
AAAATTGTTATTACCGGACACGCTGCCTGGGGAAACAGGGAATCTCTAGACCATACCCTAAAGCTATTGAGGGAGAAAAAGTAG