The EcoCyc Database (2023)
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, Markus W. Covert, Julio Collado‐Vides, Ian T. Paulsen
Abstract
. 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 online. 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 are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.