The EcoCyc database (2025)
Peter D. Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter Midford, Lisa R. Moore, Pallavi Subhraveti, Socorro Gama‐Castro, Víctor H. Tierrafría, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martínez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A. Ahn-Horst, Heejo Choi, Riley Juenemann, Cyrus N. M. Knudsen, Markus W. Covert, Julio Collado‐Vides, Ian T. Paulsen
Abstract
ABSTRACT EcoCyc is a bioinformatics database (DB) 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 was 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 product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, E. coli gene essentiality, and nutrient conditions that do or do not support the growth of E. coli . The website and downloadable software contain tools for the 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 via EcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc is also available. This review outlines the data content of EcoCyc and the procedures by which this content is generated.