The Ecoli Metabolome Database (ECMDB) is a manually curated database of small molecule metabolites found in or produced by Escherichia coli (strain K12, MG1655). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. ECMDB currently contains 2717 small molecules with 1205 associated enzymes and 299 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein.

Users may search through the ECMDB using a variety of database-specific tools. The simple text query (above) supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the “search for” field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button (on the ECMDB navigation panel above) generates a tabular synopsis of ECMDB's content. This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the ECMDB fields and sources is given here. Under the Search link (on the navigation panel above) users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the ECMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of ECMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in ECMDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. ECMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of ECMDB’s reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS, 1D NMR Spectra Search and 2D NMR Spectra Search links. Users may download ECMDB’s complete textual data, chemical structures and sequence data by clicking on the Download button.

ECMDB is supported by David Wishart, Departments of Computing Science & Biological Sciences, University of Alberta.

ECMDB is also supported by The Metabolomics Innovation Centre, a Genome Canada-funded core facility serving the scientific community and industry with world-class expertise and cutting-edge technologies in metabolomics.

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What's New?

Release 1.0 - June 1, 2011
  • Initial ECMDB release
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Please Cite:

  1. ECMDB: The E. coli Metabolome Database. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Nucleic Acids Res. 2012 Oct 29. [Epub ahead of print] PMID: 23109553

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