MetaCyc

MetaCyc provides a curated database of experimentally determined small-molecule metabolic pathways and enzymes to support analysis of metabolism across all domains of life.

Key Features:

• Pathway curation: Over 1,800 experimentally determined pathways curated from primary literature with reviews, evidence codes, and literature citations.
• Reaction–enzyme associations: Each reaction is linked to one or more well-characterized enzymes to enable detailed biochemical annotation.
• Integration with BioCyc and PGDB construction: Serves as the reference database for BioCyc, which comprises over 1,700 organism-specific Pathway/Genome Databases (PGDBs) that include an organism's full genome and predicted metabolic network constructed using MetaCyc as the reference.
• PGDB-derived predictions: PGDBs provide predicted operons, transport systems, and pathway hole-fillers to extend organism-specific metabolic models.
• Analytical tools: Support from the Pathway Tools software suite including Omics Viewers, comparative analysis tools, flux-balance analysis model generation from PGDBs, and programmatic access via web services.

Scientific Applications:

• Biochemistry: Reference for experimentally validated metabolic pathways and enzyme functions for biochemical interpretation.
• Systems biology: Basis for genome-scale metabolic network construction and flux-balance analysis modeling.
• Genomics: Annotation of organism genomes with predicted metabolic networks and enzyme–reaction mappings.
• Comparative analysis: Comparative studies of metabolic pathways and networks across species using PGDBs and comparative analysis tools.

Methodology:

Organism-specific PGDBs are constructed using MetaCyc as the reference; Pathway Tools provides Omics Viewers and comparative analysis tools, generation of flux-balance analysis models from PGDBs, and web services for programmatic access.