Karp P.D., Ong W.K., Paley S., Billington R., Caspi R., Fulcher C., Kothari A., Krummenacker M., Latendresse M., Midford P.E., Subhraveti P., Gama-Castro S., Muniz-Rascado L., Bonavides-Martinez C., Santos-Zavaleta A., Mackie A., Collado-Vides J., Keseler I.M., & Paulsen I. (2018). The EcoCyc Database. EcoSal Plus. 8(1). DOI: 10.1128/ecosalplus.ESP-0006-2018
Abstract
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coliK-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 under-standing 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 product, 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 and can be executed viaEcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.