PAMDB


NAR Molecular Biology Database Collection entry number 87
Wilks, Angela; Huang, Weiliang; Brewer, Luke; Jones, Jace; Nguyen, Angela; Marcu, Ana; Wishart, David; Oglesby-Sherrouse, Amanda; Kane, Maureen
1 Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21209, USA
2. Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada

Database Description

The Pseudomonas aeruginosaMetabolome 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.

Acknowledgements

National Institutes of Health [AI102883 to A.W.; AI123320 to A.O.S.; HD077260 to M.A.K.]; University of Maryland, School of Pharmacy, Mass Spectrometry Center [SOP1841-IQB2014]; Genome Canada and the Canadian Institutes of Health Research (to D.S.W. and A.M.).

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