Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract EcoCyc (Encyclopedia of Escherichia coli Genes and Metabolism) is a bioinformatics database that describes the genome and the biochemical machinery of E. coli.

The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli.

EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.

Products features/capabilities include:

1) Genome -- EcoCyc contains the complete genome sequence of E. coli, and describes the nucleotide position and function of every E. coli gene. A staff of five (5) full-time curators updates the annotation of the E. coli genome on an ongoing basis using a literature-based curation strategy.

Minireview summaries of E. coli gene products can be found in EcoCyc protein and RNA pages. Users can retrieve the nucleotide sequence of a gene, and the amino-acid sequence of a gene product.

2) Regulation -- EcoCyc describes several types of E. coli cellular regulation:

3) Membrane transporters -- The project is annotating E. coli transport proteins and the associated transport reactions that they mediate.

4) Metabolism -- EcoCyc describes all known metabolic pathways and signal-transduction pathways of E. coli. It describes each metabolic enzyme of E. coli, including its cofactors, activators, inhibitors, and subunit structure.

See also the MetaCyc project (see G6G Abstract Number 20232).

5) Database links -- EcoCyc is linked to other biological databases containing protein and nucleic-acid sequence data, bibliographic data, protein structures, and descriptions of different E. coli strains.

6) Literature-Based Curation -- Curation is the process of manually refining and updating a bioinformatics database. The EcoCyc project uses a literature-based curation approach in which database updates are based on evidence in the experimental literature.

EcoCyc is largely up to date with respect to its curation activities. As of April 2008, EcoCyc has encoded information from more than 16,000 publications.

7) Query and Visualization -- Scientists can use the 'BioCyc Query Page' or a 'downloadable program' to visualize the layout of genes within the E. coli chromosome, or of an individual biochemical reaction, or of a complete biochemical pathway (with compound structures displayed).

The navigation capabilities of the software allow a user to move from a display of an enzyme to a display of a reaction that the enzyme catalyzes or to the gene that encodes the enzyme.

8) Analysis of Omics Data -- EcoCyc provides software tools for the analysis of Omics datasets:

System Requirements

See G6G Abstract Number 20230 or BioCyc


Manufacturer Web Site EcoCyc

Price Contact manufacturer.

G6G Abstract Number 20231

G6G Manufacturer Number 102506