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EAWAG-BBD


NAR Molecular Biology Database Collection entry number 117
Ellis, L.B.M., Wackett, L.P.
University of Minnesota
Contact bbd@eawag.ch

Database Description

The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes.

Recent Developments

The UM-BBD has moved its data to a MySQL database. Structure-based searching has been added. The compound to be searched for can be drawn using a Java applet or entered as a SMILES string. A biochemical periodic table has been developed in traditional and spiral formats. Each element which can be biologically transformed, bound, or otherwise used has a web page describing this. A microbial metabolic pathway prediction system is being developed, based on organic functional groups, expert rules, and atom-to-atom mapping. UM-BBD users are encouraged to guide its development.

Acknowledgements

US Department of Energy

References

1. Ellis, L.B.M., Hershberger, C.D., Bryan, E.M., and Wackett, L.P. (2003) The University of Minnesota Biocatalysis/Biodegradation Database: Post-Genomic Data Mining. Nucleic Acids Res. 31: 262-265.
2. Hou, B.K., Wackett, L.P., and Ellis, L.B.M. (2003) Microbial pathway prediction: a functional group approach. J. Chem. Inform. Comp. Sci. 43: 1051-1057.
3. Wackett, L.P. and Hershberger, C.D. (2001) Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds. ASM Press, Wash. DC. xxiii+228p. ISBN 1-55581-179-5.


Subcategory: Metabolic pathways

Go to the abstract in the NAR 2006 Database Issue.
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