The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes.

Area of Science:

• Biochemistry
• Microbiology
• Bioinformatics

Background:

• The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a curated resource for microbial catabolic enzymes and metabolic pathways.
• The database contains information on over 400 enzymes, with ongoing updates and collaborations.

Purpose of the Study:

• To enhance the UM-BBD with improved enzyme information, pathway participation details, and standardized enzyme codes.
• To expand the database with specific compilations, such as reactions of naphthalene and toluene dioxygenases.
• To support microbial genome annotation and the prediction of novel metabolic pathways.

Main Methods:

• Curating and organizing data on microbial catabolic enzymes and their metabolic pathways.
• Enhancing enzyme pages with internal/external links and pathway participation information.
• Collaborating with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology to assign EC codes.
• Compiling known reactions for specific enzymes like naphthalene and toluene dioxygenases.

Main Results:

• The UM-BBD now contains information on over 400 enzymes.
• 35 UM-BBD enzymes were assigned complete EC codes in collaboration with the Nomenclature Commission.
• Compilations of reactions for naphthalene (73) and toluene (108) dioxygenases were added.
• The UM-BBD is mirrored by the European Bioinformatics Institute and KEGG.

Conclusions:

• The UM-BBD is a valuable resource for understanding microbial metabolism and enzyme function.
• Enhancements to the database facilitate the prediction of novel metabolic pathways.
• The database plays a crucial role in current microbial genome annotation efforts.