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 the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

New to EcoCyc? Take the guided tour of the Web site, watch our free online instructional videos, or read our 2013 article: "EcoCyc: fusing model organism databases with systems biology"

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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  • Card catalog

    Image of Peabody Visual Aids poster by char booth. Used under creative commons license.

    New: Search BioCyc by Locus ID

    You can now enter locus IDs into the EcoCyc quick search box. There is no need to first select the correct BioCyc organism database - if the organism is part of BioCyc, the unique locus ID will automatically find it. Some example locus IDs look like this: MSM_0046, MXAN_1061.

  • 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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  • Structures of the [4Fe-3S] cluster of H. marinus hydrogenase in the reduced (3+) and superoxidized (5+) state, Fig. 1 in Pandelia et al. (2013), PNAS 110:483-8.

    Hydrogen + Oxygen = Knallgas

    Hydrogenase 1 belongs to the special class of microbial hydrogenases that can sustain H2 oxidation in the presence of oxygen. Did you know that the the molecular basis for its oxygen tolerance relies on the unusual properties of a unique 4Fe-3S cluster?

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


  EcoCyc's sister site PortEco now hosts E. coli omics data and powerful analysis tools.

How to Cite EcoCyc

Please cite EcoCyc as Keseler et al. (2013), "EcoCyc: fusing model organism databases with systems biology", Nucleic Acids Research 41: D605-12.

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 and the Pathway Tools software. A complete list of videos in additional download formats are available on the Video and Podcast page.

This video introduces the site and the BioCyc collection of hundreds 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