title: The EcoCyc Database.
abstract: EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Carol
authors.initials: C
authors.lastname: Fulcher
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Aya
authors.initials: A
authors.lastname: Kubo
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Anamika
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authors.lastname: Kothari
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Markus
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authors.lastname: Krummenacker
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Pallavi
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authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Deepika
authors.initials: D
authors.lastname: Weerasinghe
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Araceli M
authors.initials: AM
authors.lastname: Huerta
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martinez
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Verena
authors.initials: V
authors.lastname: Weiss
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Martin
authors.initials: M
authors.lastname: Peralta-Gil
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095.|UCLA Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095.
authors.forename: Imke
authors.initials: I
authors.lastname: Schröder
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
authors.forename: Amanda
authors.initials: A
authors.lastname: Mackie
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095.
authors.forename: Robert
authors.initials: R
authors.lastname: Gunsalus
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Paulsen