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HAMAP proteomes
Escherichia coli (strain K12)

General information

Species:  Escherichia coli (strain K12)
Species code: ECOLI
Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia (TaxID: 83333) [NEWT/ NCBI]
Description: 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.

As of 2006, highly accurate sequences are available for K-12 / MG1655 and K-12 / W3110, strains that have been separate since the mid 1950s. Sequencing of PCR products indicates that there are only eight true insertion/deletion or base differences between the two strains, in addition to 13 sites where differences are due to insertion sequences, defective prophages and two sites due to the W3110 inversion between the ribosomal RNA genes rrnD and rrnE. The K-12 strains belong to phylogenetic group A.

Historically UniProtKB/Swiss-Prot considered the F plasmid to be part of the genetic makeup of strain K-12 / MG1655, whereas in fact the F plasmid was lost in a precursor strain following UV treatment and passage over blood agar. Thus we have removed the F plasmid from this genome. It can however be retrieved by searching in UniProtKB with the accession number AP001918.
Properties: Presence of flagella: Yes
Human pathogen: No
Interaction: Animal commensal in Mammalia
Number of membranes: 2

Genome(s) sequenced

Strain:    K12 / MG1655 / ATCC 47076
Genome structure:
Chromosome EMBL accession number U00096 (circular; 4,641,652 bp) (download entry)
Reference(s):
[1] Pubmed=9278503;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. ;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
Web links:
Official genome site(s):
http://www.genome.wisc.edu/
http://ecoli.aist-nara.ac.jp/
http://bmb.med.miami.edu/EcoGene/EcoWeb/
Other web sites:
BioProject: http://www.ncbi.nlm.nih.gov/bioproject/225
CBS: http://www.cbs.dtu.dk/services/GenomeAtlas/show-genus.php?kingdom=Bacteria&GLgenus=Escherichia&GLspecies=coli&GLstrain=K-12_MG1655 http://www.cbs.dtu.dk/services/GenomeAtlas/show-genus.php?kingdom=Bacteria&GLgenus=Escherichia&GLspecies=coli&GLstrain=K-12_W3110
Colibri: http://genolist.pasteur.fr/Colibri/
ECCE: http://www.cf.ac.uk/biosi/staff/ehrmann/head.html
ECDC: http://www.uni-giessen.de/ecoli/ECDC/ecdc.html
EchoBASE: http://www.biolws1.york.ac.uk/echobase/
EcoCyc: http://ecocyc.org/
EcoliWiki: http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki
ERIC: http://www.ericbrc.org/portal/eric/ecolik12mg1655
GenProtEC: http://genprotec.mbl.edu/
Micado: http://locus.jouy.inra.fr/cgi-bin/genmic/madbase/progs/madbase.operl
PEDANT: http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=analysis&Db=p3_p225_Esc_coli
 UniProtKB/Swiss-Prot document

Strain:    K12 / W3110 / ATCC 27325 / DSM 5911
Genome structure:
Chromosome EMBL accession number AP009048 (circular; 4,646,332 bp) (download entry)
Reference(s):
[1] Pubmed=16738553;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. ;
"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
Web links:
Official genome site(s):
http://ecoli.naist.jp/GB6/search.jsp
Other web sites:
CBS: http://www.cbs.dtu.dk/services/GenomeAtlas/show-genus.php?kingdom=Bacteria&GLgenus=Escherichia&GLspecies=coli&GLsupStrain=K-12&GLsubStrain=W3110
Entrez Genome Project: http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16351
ERIC: http://www.ericbrc.org/portal/eric/ecolik12w3110
PATRIC: http://patricbrc.vbi.vt.edu/portal/portal/patric/Genome?cType=genome&cId=129921
PEDANT: http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=analysis&Db=p3_p16351_Esc_coli


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