EcoCyc E. coli Database

EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.

EcoCyc is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click "change organism database" in the upper right corner to explore the available databases.

New to EcoCyc? Take the guided tour of the Web site, watch our free online instructional videos, or read our article in EcoSal (updated November 2018): "The EcoCyc Database".

EcoCyc User Guide >>
  • Cascade

    Crystal structure of E. coli Cascade. Image from the RCSB PDB ( of PDB ID 1VY8 (R.N. Jackson et al. (2014) Science 345:1473-9).

    Cascade to the Rescue!

    From protecting E. coli against phage infection to the promise of gene therapy: How does Cascade do it? Recent crystal structures of the enzyme are improving our understanding of this enzyme.

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  • Collage of E coli strains

    Except for top right (CC By 2.5) all images public domain.

    More than just K-12 MG1655

    More than 500 E. coli strain databases are available via the change organism database link (upper right corner). They are less curated than EcoCyc but work with all our website tools, from Omics Dashboard to metabolic route search.

  • Metabolic Model for E. coli K-12

    A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available.

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  • Bam complex

    Schematic diagram of the Bam complex, Fig. 1a in Kim et al.. Used under creative commons license.

    Maintaining the Outer Membrane

    The 5-subunit Bam complex is responsible for the assembly and insertion of beta-barrel proteins into the OM of E. coli. Although a full understanding of its function in beta-barrel folding remains elusive, recent work has yielded many insights into subunit interaction and activity.

  • SmartTable display generated by Pathway Tools.

    Metabolomics Data Analysis

    Multiple tools are available in this website for metabolomics data analysis.

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  • E. coli, bacteria, cryo FIB-SEM, dotted with silver nanoparticles

    BioCyc iOS App for iPhone/iPad

    EcoCyc App is now BioCyc App

    Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse EcoCyc on the go! The NEW BioCyc app comes preloaded w/ EcoCyc.

    Download Here
  • Multi-Genome Browser

    Multi-organism Genome Browser image generated by Pathway Tools.

    Comparative Genome Analysis

    Multiple comparative analysis tools are available in this website.

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  • Cellular Overview Omics Viewer image generated by Pathway Tools.

    Gene Expression Data Analysis

    Multiple tools are available in this website for analysis of gene expression data.

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EcoCyc Tools

EcoCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:

Related Sites

The E. coli Student Portal is a microbiology education site.

How to Cite EcoCyc

Please cite EcoCyc as Keseler et al. (2017), "EcoCyc: reflecting new knowledge about Escherichia coli K-12", Nucleic Acids Research 45:D543-50.

Funding Sources

The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences.

Video Tutorials

The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website.

This video introduces the site and the BioCyc collection of thousands of Pathway/Genome Databases and covers:

  • BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
  • How to search, browse, and find what you need in the BioCyc collection
  • How we represent metabolism, transcription, and all their parts