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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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The EcoCyc Database.

Peter D Karp¹, Daniel Weaver¹, Suzanne Paley¹

¹Bioinformatics Research Group, SRI International, Menlo Park, CA 94025.

|October 8, 2015

Summary

This summary is machine-generated.

EcoCyc is a comprehensive bioinformatics database detailing the Escherichia coli K-12 MG1655 genome and its biochemical machinery. It aids researchers in understanding E. coli at a system level, offering tools for data analysis and metabolic modeling.

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Area of Science:

Microbiology
Bioinformatics
Systems Biology

Background:

EcoCyc is a vital bioinformatics resource for Escherichia coli K-12 MG1655.
It aims to catalog the complete molecular components and functions within an E. coli cell.
Facilitates a systems-level comprehension of E. coli biology.

Purpose of the Study:

To provide a detailed overview of the EcoCyc database content.
To describe the methodologies used for generating and updating EcoCyc data.
To highlight the utility of EcoCyc for E. coli research and related organisms.

Main Methods:

Curated literature review and data integration for E. coli K-12 MG1655.
Development of information pages for genes, metabolites, reactions, operons, and pathways.
Generation of a steady-state metabolic flux model from each database version.

Main Results:

EcoCyc contains extensive information on E. coli genes, metabolites, reactions, and pathways.
Includes data on gene essentiality and nutrient requirements for growth.
Offers tools for high-throughput data analysis and predictive metabolic modeling.

Conclusions:

EcoCyc serves as an essential electronic reference for E. coli biologists.
The database and its associated tools support in-depth analysis and system-level understanding.
Ongoing updates and metabolic modeling enhance its value for biological research.