The EcoCyc Database

Overview

Journal EcoSal Plus

Publisher American Society for Microbiology

Specialty Microbiology

Date 2015 Oct 8

PMID 26442933

Citations 32

Authors

Peter D Karp

Daniel Weaver

Suzanne Paley

Carol Fulcher

Aya Kubo

Anamika Kothari

Markus Krummenacker

Pallavi Subhraveti

Deepika Weerasinghe

Socorro Gama-Castro

Araceli M Huerta

Luis Muniz-Rascado

Cesar Bonavides-Martinez

Verena Weiss

Martin Peralta-Gil

Alberto Santos-Zavaleta

Imke Schroder

Amanda Mackie

Robert Gunsalus

Julio Collado-Vides

Ingrid M Keseler

Ian Paulsen

Affiliations

Soon will be listed here.

Abstract

EcoCyc is a bioinformatics database 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 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, 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. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.

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