TY - JOUR
T1 - The EcoCyc Database (2023)
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, Victor H.
AU - Lara, Paloma
AU - Muñizrascado, Luis
AU - Bonavides-Martinez, César
AU - Santos-Zavaleta, Alberto
AU - Mackie, Amanda
AU - Sun, Gwanggyu
AU - Ahn-Horst, Travis A.
AU - Choi, Heejo
AU - Covert, Markus W.
AU - Collado-Vides, Julio
AU - Paulsen, Ian
PY - 2023/12
Y1 - 2023/12
N2 - EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-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 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 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.
AB - EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-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 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 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.
KW - bioinformatics
KW - database
UR - http://www.scopus.com/inward/record.url?scp=85176768413&partnerID=8YFLogxK
U2 - 10.1128/ecosalplus.esp-0002-2023
DO - 10.1128/ecosalplus.esp-0002-2023
M3 - Review article
C2 - 37220074
AN - SCOPUS:85176768413
SN - 2324-6200
VL - 11
SP - 1
EP - 22
JO - EcoSal Plus
JF - EcoSal Plus
IS - 1
ER -