TY - JOUR
T1 - The EcoCyc database (2025)
AU - Karp, Peter D.
AU - Paley, Suzanne
AU - Caspi, Ron
AU - Kothari, Anamika
AU - Krummenacker, Markus
AU - Midford, Peter E.
AU - Moore, Lisa R.
AU - Subhraveti, Pallavi
AU - Gama-Castro, Socorro
AU - Tierrafria, Víctor H.
AU - Lara, Paloma
AU - Muñiz-Rascado, Luis
AU - Bonavides-Martinez, César
AU - Santos-Zavaleta, Alberto
AU - Mackie, Amanda
AU - Sun, Gwanggyu
AU - Ahn-Horst, Travis A.
AU - Choi, Heejo
AU - Juenemann, Riley
AU - Knudsen, Cyrus N. M.
AU - Covert, Markus W.
AU - Collado-Vides, Julio
AU - Paulsen, Ian
PY - 2025/12
Y1 - 2025/12
N2 - 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.
AB - 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.
KW - bioinformatics
KW - database
KW - Escherichia coli
UR - https://www.scopus.com/pages/publications/105025018823
U2 - 10.1128/ecosalplus.esp-0019-2024
DO - 10.1128/ecosalplus.esp-0019-2024
M3 - Review article
C2 - 40304522
AN - SCOPUS:105025018823
SN - 2324-6200
VL - 13
SP - 1
EP - 28
JO - EcoSal Plus
JF - EcoSal Plus
IS - 1
ER -