Some projects of small genome sequencing have been completed, such as the archaebacterium Methanococcus jannaschii, and many pathogenic microbial genomes are underway. New proteins disclosed by the sequencing project, however, are waiting to be known their biological function and function sites. Furthermore, the new proteins from pathogenic bacteria should be targets of new drugs. Our hypothesis to find function sites is that oligopeptides which are rare in the proteins encoded by genome in a organism have specific functions, and on the contrary common oligopeptides do not have explicit function. To test this hypothesis, we have worked on DNA polymerase Pfu from the archaebacterium Pyrococcus furiosus using the genome data of M. jannaschii. We succeeded in finding the possible function sites of the enzyme by calculating the oligopeptide frequency in the whole genome data, and confirmed their importance by site-directed mutagenesis experiment.