HAMAP proteomes
Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1)

General information

Species:  Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1)
Species code: ECOD1
Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia (TaxID: 536056) [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. Strain K12 / DH1 is a derivative of strain MM294 except for the mutated alleles recA1 and gyrA96. It is a common laboratory strain used for plasmid cloning as it has a high frequency of transformation. It has been sequenced twice, in 2009, as ATCC 33849 by the JGI and a second time in 2011 in Japan as ME8569 when it was used to compare 3 next-generation sequencing techniques. The second strain had differences at 19 locations from that of DH1 ATCC 33849, including 3 single-base substitutions, 8 short nucleotide insertions and deletions, and 8 structural differences (adapted from PMID 21611185).
Properties: Presence of flagella: Yes
Human pathogen: No
Interaction: Animal commensal in Mammalia
Number of membranes: 2
Statistics: Number of ECOD1 entries in UniProtKB: 4589 (5 in UniProtKB/Swiss-Prot + 4584 in UniProtKB/TrEMBL)

Genome(s) sequenced

Strain:    ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1
Genome structure:
Chromosome EMBL accession number CP001637 (circular; 4,630,707 bp) (download entry)
Reference(s):
[1] Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ovchinnikova G., Keasling J.D. ;
"Complete sequence of Escherichia coli DH1.";
Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases.
Web links:
Entrez Genome Project: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=30031
GOLD: http://genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=Gc01118
Unofficial: http://genome.jgi-psf.org/eshcd/eshcd.info.html

Strain:    ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1
Genome structure:
Chromosome EMBL accession number AP012030 (circular; 4,621,430 bp) (download entry)
Reference(s):
[1] Pubmed=21611185;
Suzuki S., Ono N., Furusawa C., Ying B.W., Yomo T. ;
"Comparison of sequence reads obtained from three next-generation sequencing platforms.";
PLoS ONE 6:E19534-E19534(2011).
Web links:
BioProject: http://www.ncbi.nlm.nih.gov/bioproject/52077
GOLD: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=Gc01859


Tools