The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes.
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.
Ellis
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Center for Biodegradation Research and Informatics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA. lynda@tc.umn.edu
Hershberger
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CD
Bryan
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Wackett
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D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D002384:Catalysis; D016208:Databases, Factual; D004798:Enzymes / Q000235:genetics / Q000378:metabolism*; D005658:Fungi / Q000235:genetics / Q000378:metabolism; D016247:Information Storage and Retrieval; D020407:Internet
D004798:Enzymes