A simple example of how ComPath works. Glycolysis/glucogenesis pathway (A) and six gamma-proteobacteria species were selected (B). Six genomes are Escherichia coli K-12 MG1655 (eco), Escherichia coli O157 EDL933 (ece), Salmonella typhi CT18 (sty), Salmonella enterica serovar typhi Ty 2 (stt), Shigella flexneri 301 (sfl), Shigella flexneri 8401 (sfv). A possible pathway hole was found in Shigella flexneri 8401 (C). To fill in this hole, query genes were carefully chosen based on BAG clustering (D) and target genomes were selected based on clustering result (E). A candidate gene detected by CSR-HMM method was added to the table (F-H) and confirmed using three different refinement methods: Gibbs motif sampler (J), BAG clustering (K), and phylogenetic tree analysis (L). See also Figure 7.