KEGG - search & compute
KEGG pathways searched by EC numbers (enzymes), compound numbers, & by gene accessions.
Combine search with KEGG grouping or the hierarchical classification. (e.g. EC numbers from a specific group in the superfamily table (or SCOP table) & searching against pathway diagrams.
Search KEGG pathways by sequence similarity. (identify orthologs & reconstruct pathways from the gene catalog).
Given list of enzymes, automatically generate the organism specific pathways by marking the matching enzymes on the diagram. Missing elements imply either gene catalog wrong or unknown reaction pathway utilizing different enzymes in the catalog.
Compute pathways from a given list of enzymes. Deduction from binary relations of substrates and products with optional use of query relaxation for functional hierarchies.