We introduce and discuss a new computational approach towards prediction and inference of biological functions from genomic sequences by making use of the pathway data in KEGG. Due to its piecewise nature, the current approach of predicting each gene function based on sequence similarity searches often fails to reconstruct cellular functions with all necessary components. The pathway diagram in KEGG, which may be considered a wiring diagram of molecules in biological systems, can be utilised as a reference for functional reconstruction. KEGG also contains binary relations that represent molecular interactions and relations and that can be utilised for computing and comparing pathways.