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

Ellis LB, Wackett LP - Microb Inform Exp (2012)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA. lynda@umn.edu.

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.

No MeSH data available.


Structure of the UM-BBD. A solid box is UM-BBD information; a dotted box is information from one or more links to an external database.
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Figure 1: Structure of the UM-BBD. A solid box is UM-BBD information; a dotted box is information from one or more links to an external database.

Mentions: The UM-BBD database structure is shown in Figure 1. This highlights that metabolic pathways are the primary focus and consist of metabolic reactions contained on the UM-BBD server or provided to users via links to sites such as the Intermediary Metabolism database of KEGG [10]. Additional information on enzymes can also be obtained via links from UM-BBD reactions pages to the ExPASy [11], Kyoto [10], or BRENDA [12] databases. Gene sequence data can be obtained by links to the NCBI Genbank [13] database. Most pathways also list microorganisms that have been identified carry out the depicted metabolic pathways, either in full or in part.


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

Ellis LB, Wackett LP - Microb Inform Exp (2012)

Structure of the UM-BBD. A solid box is UM-BBD information; a dotted box is information from one or more links to an external database.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351732&req=5

Figure 1: Structure of the UM-BBD. A solid box is UM-BBD information; a dotted box is information from one or more links to an external database.
Mentions: The UM-BBD database structure is shown in Figure 1. This highlights that metabolic pathways are the primary focus and consist of metabolic reactions contained on the UM-BBD server or provided to users via links to sites such as the Intermediary Metabolism database of KEGG [10]. Additional information on enzymes can also be obtained via links from UM-BBD reactions pages to the ExPASy [11], Kyoto [10], or BRENDA [12] databases. Gene sequence data can be obtained by links to the NCBI Genbank [13] database. Most pathways also list microorganisms that have been identified carry out the depicted metabolic pathways, either in full or in part.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA. lynda@umn.edu.

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.

No MeSH data available.