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Welcome to the GenomeWeb Prokaryotic Genome Databases Search for:

E. coli

Other organisms

Other prokaryote genome information

Detailed information on the above options

E. coli Genome Center
The E. coli Genome Center is a laboratory of the Genetics Department, College of Agricultural and Life Sciences, at the University of Wisconsin - Madison Campus.

This is the complete sequence of the E. coli K-12 genome and several of the E. coli phages. The data is being analysed.

Functional search of the known genomes using E. coli
A tool for function keyword searching. They have built a table that relates E. Coli to Saccharomyces cerevisiae, Methanococcus jannaschii and Bacillus subtilis using blast with a Karlin Altschul score of < 10E-17. This keyword searching tool will print a list of every sequence identifier that is close to the E. Coli gene of the cluster where the keyword is found.

E.coli database collection - ECDC
In this collection you will find all information regarding the entire E.coli K12 chromosome. The collection is searchable in different ways. You can go along a gene/sequence map, scroll different tables or just search for a keyword.

EcoCyc: Encyclopedia of E. coli Genes and Metabolism
EcoCyc is a project to describe the genes and intermediary metabolism of the bacterium E. coli. It will describe each pathway and bioreaction of E. coli metabolism, and the enzyme that carries out each bioreaction, including its cofactors, activators, inhibitors, and the subunit structure of the enzyme. When known, the genes encoding the subunits of an enzyme will be listed, as well as the map position of a gene on the E. coli chromosome. In addition, the KB will describe every chemical compound involved in each bioreaction, listing synonyms for the compound name, the molecular weight of the compound, and in many cases its chemical structure.

GenProtEC - E.coli genome and proteome database
The material available on E. coli is a combination of two studies. One is a listing and categorization of E. coli gene products. The other is an update of a listing of E. coli proteins that are homologous to other E. coli proteins according to the criteria of at least 100 amino acids aligned and a PAM score of less than 200.

RegulonDB - a database on transcriptional regulation in Escherichia coli
RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in E.coli, as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. The operon is the basic structure used in RegulonDB to describe the elements and properties of transcriptional regulation. The current version contains information around 500 regulatory mechanisms, mainly for sigma 70 promoters.

Blast protein against the complete genomes of Saccharomyces, Methanococcus, E. coli and B. subtilis
This Blast interface allows you to search against two subsets of the available putative open reading frames of these genomes using blastp. A

Computational Functional Genomics
This contains comparative E. coli and Yeast Genome, Transcriptome, Proteome, Physiome and Biome data

• Comparative genome sequences
• E.coli in-frame genome engineering
• Gene clustering
• Yeast mRNA Abundance Data
• Motif software
• E.coli motifs
• E.coli Proteomics: Subcellular localization, abundance, protein sequence, ESI-MS, 2D Gels
• E.coli multiplex competition selections (phenome)

MycDB Mycobacterium Database
MycDB is intended to contain information on all aspects of mycobacteria, relevant to the study of the organisms and diseases caused by them. The focus has initially been on the molecular biology of mycobacteria, such that the database contains data on physical and genetic mapping, nucleotide sequences, and data on antigens and antibodies used in the study of the immunology of mycobacteria.

SubtiList - Bacillus subtilis genome project
This is a database dedicated to the analysis of the Bacillus subtilis genome: SubtiList.

The purpose of this database is to integrate various aspects on the genomic information of B. subtilis, the paradigm of sporulating Gram-positive bacteria. As such, it provides a clean dataset of non-redundant DNA sequences of B. subtilis (strain 168), associated to relevant annotations and protein sequences. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, keywords, location, etc.).

The data contained in SubtiList originates mainly from the B. subtilis genome sequencing project, but this dataset also benefits from the B. subtilis entries present in the EMBL/GenBank/DDBJ databanks.

Micado: MICrobial Advanced Database Organization
The database is primarily devoted to the Bacillus subtilis genome sequencing program. It links the genetic map of the microbe with its sequences, together with other bacteria. DNA comes from primary databanks entries, plus data from the SubtiList database.

NRSub: Bacillus subtilis Database
This provides access to a non-redundant set of DNA sequences from Bacillus subtilis. All the duplications from the general sequences collections have been removed and all detected overlapping sequences have been merged into contigs. Additional data on gene mapping, codon usage have been added, as cross-references with EMBL, Swiss-Prot, Enzyme, and Medline collections.

Haemophilus influenzae Rd Genome Database (HIDB)
The Haemophilus influenzae Rd genome is the first genome of a free living organism to be completed. This page offers access to the latest versions of the sequence data and related annotation.

Mycoplasma genitalium Genome Database (MGDB)
The Mycoplasma genitalium genome is the first genome of a gram positive-like bacterium to be completed. This page offers access to the latest versions of the sequence data and related annotation.

TB Genomes analysis server
The Mycobacterium tuberculosis genome analysis server.

• BLAST searches of predicted ORFS and annotated ORFS and post-blast search tools
• MYCdb web browser and data retrieval
• Three levels of query complexity/views on the Genome and its associated data
• Links to other major sites and viewers
• 'Find a gene' Using established gene names

Links for retrieved sequences allow connection to the DDBJ javaserver in Japan.

Searches can be performed to retrieve genome sequence, predicted ORFS and annotated ORFS, of both the Sanger sequenced TB genome and partial leprae genome.

CyanoBase
Synechocystis/CyanoBase provides an easy way of accessing the sequence and all-inclusive annotation data through image maps, keyword searches and the gene category list.

The cyanobacterium carries a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell.

Chlamydia Genome Project
The goal of the Chlamydia Genome Project is to determine the DNA sequence of the chromosome of Chlamydia trachomatis, serovar D (D/UW-3/Cx), trachoma biovar, and L2/434/Bu, LGV biovar. The project is a collaborative effort involving scientists at the University of California at Berkeley and Stanford University .

The WWW Virtual Library: Microbiology
This has links to many microbiology sites.

DOE Microbial Genome Initiative (MGI)
Description of the DOE Microbial Genome Initiative, including which organisms are being sequenced and who is contracted to sequence them.

Genome Information Broker for Microbial Genomes
The GIB holds information on the following genomes:

• Saccharomyces cerevisiae
• Aquifex aeolicus
• Bacillus subtilis
• Borrelia burgdorferi
• Chlamydia trachomatis
• Escherichia coli
• Haemophilus influenzae
• Helicobacter pylori
• Mycobacterium tuberculosis
• Mycoplasma genitalium
• Mycoplasma pneumoniae
• Synechocystis PCC6803
• Treponema pallidum
• Archaeoglobus fulgidus
• Methanobacterium thermoautotrophicum
• Methanococcus jannaschii
• Pyrococcus horikoshii

• Genomic View : displays genome information in diagram.
• Retrieve Clone : retrieves clone information.
• Retrieve ORF : retrieves ORF information.
• Retrieve Gene : retrieves gene information.
• Thumbnail sketch of this server : illustrates a brief overview of the server system.
• Genome sequence FTP service : Allows you to obtain nucleotide sequences.

TIGR Microbial Database
TIGR Microbial Database: a listing of microbial genomes completed and in progress.

HOBACGEN : Homologous Bacterial Genes Database
HOBACGEN is a database system that contains all the protein sequences of bacteria organized into families. It allows one to select sets of homologous genes from bacterial species and to visualize multiple alignments and phylogenetic trees. Thus HOBACGEN is particularly useful for comparative genomics, phylogeny and molecular evolution studies on bacteria.

Microbial Genomics
These microbial genome pages were created as a reference for the community and contain a list of current or completed eubacterial, archaeal and eukaryotic genome sequencing projects. Each main page includes the name of the organism being sequenced, which sequencing group(s) are involved in the effort, background information on the organism, and its current evolutionary location