Summary of Escherichia coli K-12 substr. MG1655, version 28.5 Tier 1 Highly Curated Database

Database Authors: Peter D. Karp¹, Suzanne Paley¹, Markus Krummenacker¹, Anamika Kothari¹, Ingrid Keseler¹, Ron Caspi¹, Lisa Moore¹, Ian Paulsen², Amanda Mackie², Julio Collado-Vides³, Cesar Bonavides-Martinez³, Socorro Gama-Castro³, Alberto Santos-Zavaleta³, Victor H Tierrafria³, Paloma Lara Figueroa³

¹SRI International, ²Macquarie University, ³Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico

Summary:
EcoCyc is a model-organism database for Escherichia coli K-12 MG1655. For more information, see URL EcoCyc.org.

The E. coli genome sequence used in EcoCyc has been updated from version 2 to version 3, GenBank accession number U00096.3, for release 20.0 of EcoCyc. Despite the involvement of EcoCyc staff in ongoing updates to the U00096 record, some annotation differences may be found between U00096 and EcoCyc, such as due to recent updates to EcoCyc.

Citations: [Keseler21, Karp23]

Taxonomic Lineage: cellular organisms, Bacteria <bacteria>, Pseudomonadota, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, Escherichia coli K-12 substr. MG1655

Synonyms: Escherichia coli K-12 substr. MG1655

Unification Links: GOLD:Gp0072557, NCBI-Taxonomy:511145

Organism or Sample Properties
Relationship to Oxygen:	facultative
Temperature Range:	mesophile
NCBI Genome Type:	reference

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
Chromosome	4,686	4,312	229	145	4,641,652	NCBI-GenBank:U00096.3
Genes without a physical map position:	2
Ortholog data available?	Yes

Genes:	4,686	SmartTable	Ontology
Pathways:	463	SmartTable	Ontology
Enzymatic Reactions:	2,370
Transport Reactions:	542		Ontology
Polypeptides:	4,492	SmartTable	Ontology
Protein Complexes:	1,185	SmartTable	Ontology
Enzymes:	1,453	SmartTable
Transporters:	488	SmartTable
Compounds:	3,039	SmartTable	Ontology
Transcription Units:	3,750	SmartTable	Ontology
tRNAs:	89		Ontology
Growth Media:	440		List
Transcriptional Regulation:	6,053		Ontology
Protein Features:	42,448
Phenotype Microarray Datasets:	5		List
GO Terms:	68,097		Ontology
Gene Essentiality Datasets:	6		List

Genetic Code Number:
11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)

PGDB Unique ID: 0

Copyright SRI International 1999-2023, Marine Biological Laboratory 1998-2001, DoubleTwist Inc 1998-1999. All Rights Reserved.

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References

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

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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Frontiers in Microbiology 2021
Page generated by Pathway Tools version 28.5 (software by SRI International) on Mon Jan 27, 2025, BIOCYC14A.