Yeast Metabolome Database

Yeast Metabolome Database

The Yeast Metabolome Database (YMDB) is a comprehensive, freely accessible database dedicated to the metabolome of Saccharomyces cerevisiae, commonly known as baker's or brewer's yeast. The YMDB contains detailed information about the metabolites found in yeast, including their concentrations, enzymes, reactions, and pathways.

Overview

The YMDB is a valuable resource for researchers studying yeast metabolism, providing a wealth of information about the metabolites present in yeast cells. The database includes data on over 2000 metabolites, 900 enzymes, and 700 reactions, as well as information on the pathways in which these metabolites, enzymes, and reactions are involved.

Content

Metabolites

The YMDB contains information on a wide range of metabolites found in yeast, including amino acids, nucleotides, carbohydrates, lipids, and secondary metabolites. For each metabolite, the database provides a variety of information, including its chemical structure, molecular weight, and physicochemical properties.

Enzymes

The database also includes information on the enzymes that catalyze the reactions involving these metabolites. This includes data on the enzyme's name, classification, and the reactions it catalyzes.

Reactions

The YMDB provides detailed information on the reactions that occur in yeast metabolism. This includes data on the reactants, products, and enzymes involved in each reaction.

Pathways

The database also includes information on the pathways in which these metabolites, enzymes, and reactions are involved. This includes data on the pathway's name, the reactions that occur within it, and the metabolites and enzymes involved in these reactions.

Accessing the Database

The YMDB is freely accessible online and can be searched using a variety of criteria, including metabolite name, enzyme name, reaction name, and pathway name. The database also includes a variety of tools for analyzing and visualizing the data.

Applications

The YMDB is a valuable resource for researchers studying yeast metabolism. It can be used to identify the metabolites present in a particular sample, to study the reactions and pathways involved in yeast metabolism, and to develop computational models of yeast metabolism.

See Also

• Saccharomyces Genome Database
• Bioinformatics
• Metabolomics

References

• Jewison, T., Knox, C., Neveu, V., Djoumbou, Y., Guo, A. C., Lee, J., ... & Wishart, D. S. (2012). YMDB: the Yeast Metabolome Database. Nucleic acids research, 40(D1), D815-D820.
• Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., ... & Scalbert, A. (2013). HMDB 3.0—The Human Metabolome Database in 2013. Nucleic acids research, 41(D1), D801-D807.