PAMDB: A comprehensive Pseudomonas aeruginosa metabolome database
Date
2018Journal
Nucleic Acids ResearchPublisher
Oxford University PressType
Article
Metadata
Show full item recordAbstract
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.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/10713/9439ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkx1061
Scopus Count
Collections
Related articles
- YMDB: the Yeast Metabolome Database.
- Authors: Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P, Mandal R, Krishnamurthy R, Sinelnikov I, Wilson M, Wishart DS
- Issue date: 2012 Jan
- ECMDB: the E. coli Metabolome Database.
- Authors: Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS
- Issue date: 2013 Jan
- HMDB: the Human Metabolome Database.
- Authors: Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L
- Issue date: 2007 Jan
- Exploring human metabolites using the human metabolome database.
- Authors: Forsythe IJ, Wishart DS
- Issue date: 2009 Mar
- HMDB: a knowledgebase for the human metabolome.
- Authors: Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I
- Issue date: 2009 Jan