The EcoCyc database

Peter D. Karp*, Daniel Weaver, Suzanne Paley, Carol Fulcher, Aya Kubo, Anamika Kothari, Markus Krummenacker, Pallavi Subhraveti, Deepika Weerasinghe, Socorro Gama-Castro, Araceli M. Huerta, Luis Muñiz-Rascado, César Bonavides-Martinez, Verena Weiss, Martin Peralta-Gil, Alberto Santos-Zavaleta, Imke Schröder, Amanda Mackie, Robert Gunsalus, Julio Collado-VidesIngrid M. Keseler, Ian Paulsen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

40 Citations (Scopus)

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 longterm 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.

Original languageEnglish
Pages (from-to)1-13
Number of pages13
JournalEcoSal Plus
Volume6
Issue number1
DOIs
Publication statusPublished - 2014

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