ComPath is a web-based sequence analysis system built upon KEGG (Kyoto Encyclopedia of Genes and Genomes) and PLATCOM (Platform for Computational Comparative Genomics). Upon selection of a pathway and any combination of genomes in KEGG, an enzyme-genome table is created and users can use the table for various enzyme sequence analysis tasks.

It allows for tests on whether a certain enzyme in a given pathway is present or missing using sequence analysis techniques, namely, (a) pairwise/multiple sequence alignment, (b) phylogenetic analysis of enzymes in selected genomes, (c) domain-based analysis using hidden markov models (HMM), (d) sequence analysis using SCOPEC superfamily and PDB domains and (e) Gibbs motif sampler.

Users can also upload their sequence set, e.g., an entire set of predicted proteins in a newly sequenced genome, and perform annotation of the sequences in terms of KEGG pathways. ComPath is being extended to incorporate more resources, including protein structure information. In particular, we are developing databases and algorithms for enzyme analysis, e.g., classifiers using a database of enzyme-specific HMMs. ComPath is in an early stage of system development and we solicit feedback and suggestions from biology and bioinformatics communities.