• More than just K-12 MG1655

    More than 500 E. coli strain databases are available via the "Change Current Database" button above. They are less curated than EcoCyc but work with all our website tools, from Omics Dashboard to metabolic route search.

    Collage of E coli strains

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

  • Route Search Diagram

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    RouteSearch: Search for Paths through the Metabolic Network

    Search for lowest-cost paths through the metabolic network of the selected organism. Or, design lowest-cost pathways to novel compounds by adding reactions from MetaCyc.

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  • 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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    Cascade

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

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

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    Diagram of metabolic model

    Metabolic Model for E. coli K-12

  • 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.

    Bam complex

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

  • Metabolomics Data Analysis

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

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    Dialog for specifying parameters in an enrichment analysis

    SmartTable display generated by Pathway Tools.

  • Comparative Genome Analysis

    Multiple comparative analysis tools are available in this website.

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    Multi-Genome Browser

    Multi-organism Genome Browser image generated by Pathway Tools.

  • Gene Expression Data Analysis

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

    Learn More
    WebOmics Image

    Cellular Overview Omics Viewer image generated by Pathway Tools.

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 Current Database" above to explore the available databases.

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

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Learning Library

Webinar Series

Webinar #1: Introduction to BioCyc
These six sequential segments, giving you a guided tour of the BioCyc collection in concise bites. To download or view, just click on one of the links following each segment's name.
Webinar #2: Introduction to SmartTables
The following webinar will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The webinar is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below.
Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This webinar introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
Webinar #4: Omics Data Analysis
This webinar will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Webinar #5: Pathway Collages
Pathway collages are multi-pathway diagrams that you can customize by, for example, overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. Learn how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways.
Webinar #6: Creating a Pathway/Genome Database
Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB) for an organism with a sequenced and annotated genome. Build a PGDB for your own lab or for the whole scientific community.
Webinar #7: Using the Structured Advanced Query Page
An introduction to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. You'll learn about:The basic steps of setting up an advanced query; Four examples of increasingly complex queries, including how to query across multiple databases; Where to learn more about the structure of BioCyc databases.