UM-BBD

UM-BBD provides a curated database of biodegradation and biocatalysis information to support research on microbial degradation pathways of organic compounds.

Key Features:

• Content scope: Contains detailed entries for nearly 1,200 compounds, over 800 enzymes, approximately 1,300 reactions, and close to 500 microorganism records.
• Biochemical Periodic Table (UM-BPT): Organizes biochemical data in a systematic table focused on biocatalytic elements and reactions.
• Pathway Prediction System (UM-PPS): Implements a rule-based system to predict plausible metabolic pathways for microbial degradation of organic compounds.
• Biotransformation rules: Encodes 260 biotransformation rules derived from UM-BBD reaction data and scientific literature.
• Data integration: Contributes compound data to public chemical databases such as PubChem and ChemSpider.

Scientific Applications:

• Microbial metabolism research: Supports investigation of microbial degradation pathways for organic compounds.
• Bioremediation strategy design: Informs the development of bioremediation approaches for contaminated environments.
• Synthetic biology and biocatalysis: Provides reference data for engineering novel biocatalytic pathways and enzyme functions.
• Pathway prediction and hypothesis generation: Enables generation of plausible biodegradation routes using rule-based predictions.

Methodology:

Data compilation of compounds, enzymes, reactions, and microorganisms; organization of biochemical information via UM-BPT; rule-based pathway prediction in UM-PPS using 260 biotransformation rules derived from UM-BBD reaction data and scientific literature.