BKMS-react

BKMS-react compiles a non-redundant, integrated database of biochemical reactions to support reconstruction and analysis of genome-scale metabolic networks and enzyme-focused research.

Key Features:

• Integrated data sources: Aggregates reaction data extracted from BRENDA, KEGG, MetaCyc, and SABIO-RK.
• Reaction coverage: Contains 18,172 unique biochemical reactions.
• Reaction types: Includes both enzyme-catalyzed and spontaneous reactions.
• Two-step matching: Aligns substrates and products using a two-step comparison based on structural representations (InChIs) and molecule names.
• Non-redundant harmonization: Harmonizes variable reaction annotations into a unified, non-redundant reaction set.
• Enzyme classification support: Accounts for recent enzyme classification updates, including EC 7 translocases.
• Complement to BRENDA: Serves as a reaction-centric complement to BRENDA, which contains over 4.3 million entries related to approximately 84,000 enzymes.
• Pathway connectivity data: Provides information linking reactions to pathway connections.

Scientific Applications:

• Genome-scale metabolic network reconstruction: Supplies consolidated reaction sets to improve accuracy of metabolic model construction.
• Pathway analysis: Supports mapping and analysis of pathway connections using integrated reaction data.
• Enzyme research and annotation: Aids enzyme-centric studies and annotation by providing harmonized reaction information across databases.
• Cross-database harmonization: Enables comparison and consolidation of reaction annotations from multiple biochemical databases.

Methodology:

Reactions are extracted from BRENDA, KEGG, MetaCyc, and SABIO-RK and integrated by aligning substrates and products through a two-step comparison using structural representations (InChIs) and molecule names, followed by harmonization into a unified, non-redundant reaction set.