Yeast metabolite structures, metabolite descriptions, metabolite reactions, metabolite enzymes and transporters, yeast enzyme and transporter sequences, chemical properties, nomenclature, synonyms, chemical taxonomy, metabolite NMR spectra, metabolite GC-MS spectra, metabolite LC-MS spectra
Contact
Research center
University of Alberta and The Metabolomics Innovation Centre
Laboratory
David S. Wishart
Primary citation
The Yeast Metabolome Database.[1]
Access
Website
http://www.ymdb.ca
Download URL
http://www.ymdb.ca/downloads
Miscellaneous
Data release frequency
Every 2-3 years with periodic corrections and updates
Curation policy
Manually curated
The Yeast Metabolome Database (YMDB)[1] is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast metabolomics research, specifically in the areas of general fermentation as well as wine, beer and fermented food analysis. YMDB supports the identification and characterization of yeast metabolites using NMR spectroscopy, GC-MS spectrometry and Liquid chromatography–mass spectrometry (LC-MS spectrometry). The YMDB contains two kinds of data: 1) chemical data and 2) molecular biology/biochemistry data. The chemical data includes 2027 metabolite structures with detailed metabolite descriptions along with nearly 4000 NMR, GC-MS and LC/MS spectra.
The biochemical data includes 1104 protein (and DNA) sequences and more than 900 biochemical reactions (Fig. 1) that are linked to these metabolite entries.[1] Each metabolite entry in the YMDB contains more than 80 data fields with 2/3 of the information being devoted to chemical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, Protein Data Bank, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The YMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches.
The YeastMetabolomeDatabase (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced...
biofluid-specific metabolomedatabases. Some of the better known metabolomedatabases include the Human MetabolomeDatabase or HMDB, the YeastMetabolomeDatabase or...
www.emolecules.com. Retrieved 2020-07-27. "Human MetabolomeDatabase: About the Human MetabolomeDatabase". hmdb.ca. Retrieved 2020-07-27. Van Santen, Jeffrey...
PMC 5801651. PMID 28190004. "Megastigmatrienone (YMDB01739)". YeastMetabolomeDatabase. Archived from the original on 15 January 2020. Retrieved 27 February...
on YeastMetabolomeDatabase Morata, A; González, C; Suárez-Lepe, JA (2007). "Formation of vinylphenolic pyranoanthocyanins by selected yeasts fermenting...
articles. Bovine MetabolomeDatabase is a free web database that lists known bovine metabolites Wren JD, Bateman A (October 2008). "Databases, data tombs and...
albicans or other yeast/fungus species. Merck Index, 11th Edition, 789 "2-Carb-19". Arabitol at the Human MetabolomeDatabase "Candida and Yeast Overgrowth"...
leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue...
biological fields of study; it is complementary to the proteome and the metabolome and encompasses the translatome, exome, meiome and thanatotranscriptome...
that break down the proteins in the grain into forms that can be used by yeast. The point at which the malting process is stopped affects the starch-to-enzyme...
Storey Books. pp. 64–67. ISBN 978-0-88266-940-3. "Diacetyl". E. coli MetabolomeDatabase. ECMDB. Archived from the original on 20 October 2013. Retrieved...
ultra low concentrations. Databases such as neXtprot and UniProt are central resources for human proteomic data. Metabolome Cytome Bioinformatics List...
PMC 4678511. PMID 26435376. "Adenosine monophosphate". The Human MetabolomeDatabase. Retrieved 3 July 2020. Baker, Julien S.; McCormick, Marie Clare;...
the objects of study of such fields, such as the genome, proteome, or metabolome (lipidome) respectively. The suffix -ome as used in molecular biology...
can explore MetPA's output using three different views or levels: 1) a metabolome view; 2) a pathway view; 3) a compound view. As noted above MetPA performs...
sporogenes. IPA metabolism diagram "3-Indolepropionic acid". Human MetabolomeDatabase. University of Alberta. Retrieved 12 June 2018. Chyan YJ, Poeggeler...
of Molecular Plant Physiology in Golm Database (19 July 2007). "Glucose mass spectrum". Golm MetabolomeDatabase. Archived from the original on 9 September...
effects because it causes a detrimental impact on the gut microbiota and metabolome. It should only be used for short periods of time and under the advice...
within a cell, tissue, organism, or ecosystem and is a subset of the "metabolome" which also includes other major classes of biological molecules (such...
Wayback Machine, accessed: January 12, 2007. "Diacetyl". E.coli MetabolomeDatabase. ECMDB. Retrieved 20 October 2013. D. Sogg "White Wines, New Barrels:...
Global Information