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Escherichia coli Databases
EcoCyc EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K-12 MG1655. 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. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
Ecogene 2.0 EcoGene 2.0, release date March 1, 2007, is the first monthly release of the new EcoGene. It is a continuation of EcoGene 1 to EcoGene 19, and thus would have been EcoGene 20. Monthly release archival downloads are now available through the Downloads page, but please note that the live, daily updated version of EcoGene is the default mysql database for download queries. The old EcoGene (bmb.med.miami.edu) is closed, and links to the old EcoGene are being directed to www.ecogene.org.
GenProtEC GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit. Our annotation work includes multiple types of information:
1. Sequence similarity to orthologues as defined by Darwin (start and end of aligned region, identity, and PAM distance).
2. Resolution of fused proteins into modular units with independent functions.
3. Identification of sequence similar protein groups within E. coli that are clustered by transitive relationships. The sequence similarity is limited to PAM 200 and an alignment of at least 83 amino acids.
4. Updated literature references.
5. Classification of gene products by their gene type and by their cellular role(s). The MultiFun classification system for cellular roles is used to assign gene products to one or more roles. MultiFun has been converted to Gene Ontology terms.
6. Familes of proteins related by structure and biochemical reaction mechanisms (work in progress).
7. SCOP superfamily identification and location (e.g. binding site domains) for E. coli proteins.
JCVI CMR The Comprehensive Microbial Resource (CMR) is a free website maintained by J. Craig Venter Institute (JCVI), used to display information on all of the publicly available, complete prokaryotic genomes. In addition to the convenience of having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. A CMR Mirror site maintained by the Genome Encyclopedia of Microbes (GEM) in Korea is also available. The present link is to the E. coli K12 genome on the CMR website.
Genomics and Proteomics Tools
Phyre
3D-Jury
meta-PPISP

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