The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining

• Published in: Nucleic acids research Vol. 31; no. 1; pp. 262 - 265
• Main Authors: Ellis, Lynda B. M., Hou, Bo Kyeng, Kang, Wenjun, Wackett, Lawrence P.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2003
• Subjects: Biodegradation; Biodegradation, Environmental; Biotransformation; Catalysis; Databases, Factual; Environmental Pollutants - metabolism; Genomics; metalloids; Metals - metabolism; Minnesota; Prokaryotic Cells - metabolism; Minnesota
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg048

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.