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Overview

Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome_redundancy">more...</a>)</p> 4,605
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000009182
Taxonomy362663 - Escherichia coli O6:K15:H31 (strain 536 / UPEC)
Strain536 / UPEC
Last modifiedMarch 7, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000013305.1 from ENA/EMBL full
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:99.1%[S:98.6%,D:0.5%],F:0.2%,M:0.7%,n:440 enterobacterales_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Close to standard (low value)

Escherichia coli is a Gram-negative straight rod, which either uses peritrichous flagella for mobility or is nonmotile. It is a facultatively anaerobic chemoorganotroph capable of both respiratory and fermentative metabolism. E.coli serves a useful function in the body by suppressing the growth of harmful bacterial species and by synthesising appreciable amounts of vitamins. It is an important component of the biosphere. It colonizes the lower gut of animals and survives when released to the natural environment, allowing widespread dissemination to new hosts. Pathogenic E.coli strains are responsible for infection of the enteric, urinary, pulmonary and nervous systems. Comparison of 20 E.coli/Shigella strains shows the core genome to be about 2000 genes while the pan-genome has over 18,000 genes. There are multiple, striking integration hotspots that are conserved across the genomes, corresponding to regions of abundant and parallel insertions and deletions of genetic material.

The uropathogenic Escherichia coli (UPEC) strain 536 was originally isolated from a patient with acute pyelonephritis. Strain 536 (O6:K15:H31) is one of the model organisms of extraintestinal E. coli. The genome consists of a circular chromosome of 4.9 Mbp, and harbors 5 well characterized pathogenicity islands and a newly identified sixth island, encoding the key virulence factors of this strain. Excision of 4 of the 6 islands was observed. It belongs to phylogroup B2.

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Chromosome4605

Publications

  1. "Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536."
    Hochhut B., Wilde C., Balling G., Middendorf B., Dobrindt U., Brzuszkiewicz E., Gottschalk G., Carniel E., Hacker J.
    Mol. Microbiol. 61:584-595(2006) [PubMed] [Europe PMC] [Abstract]
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