The EcoCyc Database.

Q1 Medicine EcoSal Plus Pub Date : 2018-11-01 DOI:10.1128/ecosalplus.ESP-0006-2018
Peter D Karp, Wai Kit Ong, Suzanne Paley, Richard Billington, Ron Caspi, Carol Fulcher, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Pallavi Subhraveti, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Julio Collado-Vides, Ingrid M Keseler, Ian Paulsen
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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 product, 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 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. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.

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EcoCyc 数据库。
EcoCyc 是一个生物信息学数据库,可在 EcoCyc.org 上查阅,该数据库描述了大肠杆菌 K-12 MG1655 的基因组和生化机制。该项目的长期目标是描述大肠杆菌细胞的完整分子目录及其每个分子部分的功能,以促进对大肠杆菌的系统级了解。EcoCyc 是大肠杆菌生物学家以及从事相关微生物研究的生物学家的电子参考源。该数据库包括每个大肠杆菌基因产物、代谢物、反应、操作子和代谢途径的信息页面。数据库还包括有关大肠杆菌基因本质和支持或不支持大肠杆菌生长的营养条件的信息。网站和可下载软件包含用于分析高通量数据集的工具。此外,每个新版本的 EcoCyc 都会生成一个稳态代谢通量模型,可通过 EcoCyc.org 执行。该模型可预测不同基因敲除和营养条件下的代谢通量率、营养吸收率和生长率。本综述概述了 EcoCyc 的数据内容以及生成这些内容的程序。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
EcoSal Plus
EcoSal Plus Immunology and Microbiology-Microbiology
CiteScore
12.20
自引率
0.00%
发文量
4
期刊介绍: EcoSal Plus is the authoritative online review journal that publishes an ever-growing body of expert reviews covering virtually all aspects of E. coli, Salmonella, and other members of the family Enterobacteriaceae and their use as model microbes for biological explorations. This journal is intended primarily for the research community as a comprehensive and continuously updated archive of the entire corpus of knowledge about the enteric bacterial cell. Thoughtful reviews focus on physiology, metabolism, genetics, pathogenesis, ecology, genomics, systems biology, and history E. coli and its relatives. These provide the integrated background needed for most microbiology investigations and are essential reading for research scientists. Articles contain links to E. coli K12 genes on the EcoCyc database site and are available as downloadable PDF files. Images and tables are downloadable to PowerPoint files.
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