ECMDB: The E. coli Metabolome Database

  1. Get@NRC: ECMDB: The E. coli Metabolome Database (Opens in a new window)
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Journal titleNucleic Acids Research
Subjectbacterial enzyme; bacterial protein; amino acid sequence; bacterial gene; bacterial growth; bacterial metabolism; bacterial strain; bioinformatics; carbon nuclear magnetic resonance; chemical structure; Escherichia coli; factual database; gene sequence; mass spectrometry; metabolite; metabolome; molecular weight; proton nuclear magnetic resonance; Databases, Genetic; Escherichia coli K12; Escherichia coli Proteins
AbstractThe Escherichia coli Metabolome Database (ECMDB, is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry. © The Author(s) 2012.
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AffiliationNational Research Council Canada (NRC-CNRC); Security and Disruptive Technologies
Peer reviewedYes
NPARC number21271842
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Record identifier0d7350c5-aea6-4ecb-a7eb-3fdd3509705f
Record created2014-04-23
Record modified2016-05-09
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