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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%5Fredundancy">more...</a>)</p> 4,156
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%5Fmanual">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>UP000002032
Taxonomy469008 - Escherichia coli (strain B / BL21-DE3)
StrainB / BL21-DE3 [JGI]
Last modifiedJanuary 1, 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_000023665.1 from ENA/EMBL full
Pan proteomei <p>A pan proteome is the full set of proteins thought to be expressed by a group of highly related organisms (e.g. multiple strains of the same bacterial species).<p><a href='/help/pan_proteomes' target='_top'>More...</a></p> This proteome is part of the Escherichia coli (strain K12) pan proteome (fasta)
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 (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:100%[S:99.5%,D:0.5%],F:0%,M:0%,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)

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.

Escherichia coli B serves as a research model for studying phage sensitivity, restriction-modification systems, and bacterial evolution, and also as a workhorse for protein expression in life science laboratories and in the biotech industry. Characteristics such as protease deficiency, low acetate production at a high level of glucose, and enhanced permeability (probably due to a simple cell surface) make E. coli B a desirable host for the production of genetically engineered proteins. BL21(DE3) has been very widely used to express recombinant proteins. Comparison of BL21(DE3) and another B strain REL606 (ECOBR) shows they differ in length by 72,304 bp and have 426 single nucleotide polymorphisms, all of which have been accounted for by various laboratory manipulations. Differences between B strains and K12 include the absence of flagellar component genes, the DNA cytosine methylase dcm, and ompT in BL21(DE3). B strains may have an additional type II secretion system not found in K12. Other differences include differential distribution of insertions sequences and other changes resulting from horizontal gene transfer. BL21(DE3) also carries a DE3 recombinant phage harboring the T7 RNA polymerase gene that can direct high-level expression of cloned genes under the control of the T7 promoter (adapted from PMID 19786035).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome4156

Publications

  1. "Complete sequence of Escherichia coli BL21(DE3)."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., LaButti K.M., Clum A., Larimer F., Land M., Hauser L., Kyrpides N., Anderson I., Sorek R., Rubin E.
    Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases
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Main funding by: National Institutes of Health

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