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Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

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ECMDB: the E. coli Metabolome Database.

An Chi Guo¹, Timothy Jewison, Michael Wilson

¹Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.

Nucleic Acids Research

|October 31, 2012

Summary

This summary is machine-generated.

The Escherichia coli Metabolome Database (ECMDB) provides comprehensive data on over 2600 metabolites, linking them to genes and proteins. This resource aids researchers in understanding E. coli

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Area of Science:

Metabolomics
Systems Biology
Bioinformatics

Background:

Escherichia coli (E. coli) is a crucial model organism in biology and a key player in industrial biotechnology.
A comprehensive, curated database of E. coli's metabolome is essential for research and development.

Purpose of the Study:

To develop and present the Escherichia coli Metabolome Database (ECMDB).
To consolidate and provide access to extensive data on E. coli metabolites, genes, proteins, and associated information.

Main Methods:

Compiled data from textbooks, journals, and electronic databases.
Integrated information on >2600 metabolites, ∼1500 genes/proteins, reactions, and pathways.
Included experimental data: metabolite concentrations, NMR, and mass spectrometry spectra.

Main Results:

The ECMDB contains >2600 metabolites with detailed annotations (average 75 data fields per metabolite).
Entries link metabolites to genes, proteins (enzymes, transporters), reactions, and pathways.
Database includes metabolite concentration data and spectral information (NMR, MS).

Conclusions:

The ECMDB serves as a valuable resource for metabolomics, molecular biology, and systems biology research.
The database supports E. coli research and its applications in the biotechnology industry.
Advanced search and browsing tools facilitate data exploration and discovery.