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Open Access Review

Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation

Lynda BM Ellis1* and Lawrence P Wackett23

Author Affiliations

1 Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA

2 BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA

3 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN 55108, USA

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Microbial Informatics and Experimentation 2012, 2:1  doi:10.1186/2042-5783-2-1

Published: 4 January 2012

Abstract

Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial biodegradative metabolism is the main focus of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD). UM-BBD data has also been used to develop a computational metabolic pathway prediction system that can be applied to chemicals for which biodegradation data is currently lacking. The UM-Pathway Prediction System (UM-PPS) relies on metabolic rules that are based on organic functional groups and predicts plausible biodegradative metabolism. The predictions are useful to environmental chemists that look for metabolic intermediates, for regulators looking for potential toxic products, for microbiologists seeking to understand microbial biodegradation, and others with a wide-range of interests.

Keywords:
Biodegradation database; pathway prediction; microbial degradation