Tier 1 Highly Curated Organism Database
Escherichia coli K-12 substr. MG1655
Database Authors
Summary EcoCyc is a model-organism database for Escherichia coli K-12 MG1655, the strain from which the first complete genome sequence was obtained for E. coli [Blattner97]. The source of the original K-12 isolate came from a stool sample from a patient with diptheria in 1922, but the name, K-12, is more difficult to pin down (see Microbiology Today, Escherichia coli and Small Things Considered, How did E. coli get named K-12?).

The genome sequences used in EcoCyc have been updated from the original Blattner et al. sequence through a collaboration between EcoCyc, the University of Wisconsin, UniProtKB/Swiss-Prot, and the National Center for Biotechnology Information (NCBI). The E. coli genome sequence used in EcoCyc currently was updated from version 2 to version 3, GenBank accession number U00096.3, at release 20.0 of EcoCyc. Annotation updates to the NCBI U00096.3 from EcoCyc are ongoing. However, despite the involvement of EcoCyc staff in these ongoing updates to the U00096 record, some annotation differences may be found, such as due to recent updates to EcoCyc.

EcoCyc also collaborates with the Gene Ontology Consortium and UniProtKB to maintain consistency between the databases.

For more information, see EcoCyc.org and the link to Project Overview.

Citations: [Keseler21, Karp23]

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 4,541 4,312 229 146 4,641,652 GenBank:U00096.3
Genes without a physical map position:
Ortholog data available? Yes
Database Contents
Genes 4,687
Pathways 480
Enzymatic Reactions 2,426
Transport Reactions 549
Polypeptides 4,491
Protein Complexes 1,204
Enzymes 1,456
Transporters 490
Compounds 3,081
Transcription Units 3,767
tRNAs 89
Growth Media 441
Transcriptional Regulation 6,102
Protein Features 45,016
Phenotype Microarray Datasets 5
GO Terms 74,214
Gene Essentiality Datasets 6
Database Version29.1 [History of Updates]
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli K-12
Escherichia coli K-12 substr. MG1655
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLDGp0072557
NCBI-Taxonomy511145
Geographic LocationPalo Alto, CA
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipsymbiont
Pathogenicityhuman
HostHomo sapiens
NCBI Genome Typereference
Copyright SRI International 1999-2023, Marine Biological Laboratory 1998-2001, DoubleTwist Inc 1998-1999. All Rights Reserved.

References

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

Karp23: Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muniz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J, Paulsen I (2023). "The EcoCyc Database (2023)." EcoSal Plus 11(1);eesp00022023. PMID: 37220074

Keseler21: Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martinez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muniz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafria VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD (2021). "The EcoCyc Database in 2021." Front Microbiol 12;711077. PMID: 34394059

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Frontiers in Microbiology 2021
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