PathPred

PathPred predicts multi-step enzymatic reaction pathways from a query compound using RDM patterns and chemical structure alignments to elucidate microbial biodegradation and plant secondary metabolite biosynthesis.

Key Features:

• KEGG RPAIR / RDM patterns: Uses the KEGG RPAIR database containing RDM (Reaction Description Model) patterns and chemical structure alignments of substrate–product pairs documented in Enzyme Nomenclature and KEGG PATHWAY.
• Local RDM pattern matching: Identifies characteristic local RDM pattern matches between the query compound and reactant pairs.
• Global chemical structure alignment: Performs global chemical structure alignments of substrate–product pairs against a library of reactant pairs.
• Reactant-pair libraries: Employs a library composed of 947 reactant pairs associated with biodegradation and 1397 reactant pairs linked to biosynthesis.
• Multi-step pathway generation: Predicts transformed compounds at each reaction step and assembles plausible multi-step pathways from matched transformations.
• Reference transformation patterns: Provides reference transformation patterns that explain the structural changes for each predicted reaction.
• Output representation: Outputs predicted multi-step reaction pathways as a tree-shaped graph representing alternative transformation routes.
• Biological focus: Emphasizes microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites.

Scientific Applications:

• Biodegradation pathway prediction: Predicts plausible enzymatic pathways for microbial degradation of environmental compounds.
• Secondary metabolite biosynthesis: Predicts biosynthetic pathways for plant secondary metabolites.
• Elucidation of enzymatic transformations: Provides transformation patterns and stepwise compound predictions to clarify enzyme-catalyzed reaction mechanisms documented in Enzyme Nomenclature and KEGG PATHWAY.

Methodology:

Matches local RDM patterns and performs global chemical structure alignments against the KEGG RPAIR reactant-pair library (947 biodegradation pairs, 1397 biosynthesis pairs) derived from Enzyme Nomenclature and KEGG PATHWAY, analyzes RDM patterns to generate transformed compounds and reference transformation patterns, and outputs predicted multi-step pathways as a tree-shaped graph.