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    PAMDB: A comprehensive Pseudomonas aeruginosa metabolome database

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    Author
    Huang, W.
    Brewer, L.K.
    Jones, J.W.
    Date
    2018
    Journal
    Nucleic Acids Research
    Publisher
    Oxford University Press
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://dx.doi.org/10.1093/nar/gkx1061
    Abstract
    The Pseudomonas aeruginosa Metabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. Copyright 2017 The Author(s).
    Sponsors
    National Institutes of Health [AI102883, AI123320, HD077260, University of Maryland, School of Pharmacy, Mass Spectrometry Center [SOP1841-IQB2014]; Genome Canada and the Canadian Institutes of Health Research.
    Keyword
    PAMDB
    Metabolome
    Pseudomonas aeruginosa
    Database
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040864762&doi=10.1093%2fnar%2fgkx1061&partnerID=40&md5=7133f2efcaa8b3408dd2935a3abd2387; http://hdl.handle.net/10713/9439
    ae974a485f413a2113503eed53cd6c53
    10.1093/nar/gkx1061
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