The EcoCyc database (2025)

Area of Science:

• Microbiology
• Bioinformatics
• Systems Biology

Background:

• EcoCyc is a bioinformatics database detailing the genome and biochemical machinery of Escherichia coli K-12 MG1655.
• It serves as an electronic reference for E. coli biologists and researchers working with related microorganisms.

Purpose of the Study:

• To describe the complete molecular catalog of the E. coli cell and the functions of its molecular parts.
• To facilitate a system-level understanding of E. coli.
• To provide tools for analyzing high-throughput data sets.

Main Methods:

• Curating and integrating data on E. coli genes, products, metabolites, reactions, operons, and pathways.
• Incorporating information on gene expression regulation, essentiality, and growth conditions.
• Developing and utilizing a steady-state metabolic flux model and a whole-cell model.

Main Results:

• The database contains detailed information pages for E. coli gene products, metabolites, reactions, operons, and metabolic pathways.
• Includes data on gene regulation, essentiality, and nutrient requirements for growth.
• A metabolic flux model predicts flux rates, nutrient uptake, and growth rates for various conditions and gene knockouts.

Conclusions:

• EcoCyc provides a valuable, integrated resource for E. coli research.
• The database and associated models facilitate systems-level analysis and prediction of cellular behavior.
• It supports diverse research applications, from basic biology to metabolic engineering.