The EcoCyc Database.
The EcoCyc Database.
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DOI：
10.1128/ecosalplus.esp-0006-2018
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发表时间：
2018-11-01
期刊：
影响因子：
--
通讯作者：
Paulsen, Ian
中科院分区：
文献类型：
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作者：
Karp, Peter D;Ong, Wai Kit;Paulsen, Ian
EcoCyc是一个生物信息学数据库，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，以及其每个分子部分的功能，以促进对大肠杆菌的系统级理解。EcoCyc是大肠杆菌生物学家和从事相关微生物工作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、操纵子和代谢途径的信息页面。该数据库还包括大肠杆菌基因的重要性以及支持或不支持大肠杆菌生长的营养条件的信息。该网站和可下载的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都会生成稳态代谢通量模型，并可通过EcoCyc.org执行。该模型可以预测不同基因敲除和营养条件下的代谢通量率、营养摄取率和生长率。本综述概述了EcoCyc的数据内容以及生成这些内容的程序。
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.