The exponential growth of genome sequences and rapid advances in automatic annotation services provide a vast of resources for researchers. Consequently, the integration of these diverse sources of biological information is a major priority. One of the most rapidly increasing information sources represents data describing metabolism and regulatory pathways that act as the intermediate of bio-molecules, and their functions in complex activities in the cell. We report our work on the integration of the KEGG pathway database, the KEGG Orthology (KO) and the Molecular Interaction (MINT) database based on the Chado schema. Using this consolidated database, we have developed a pathway comparison tool that can identify differences in terms of proteins that are present or missing in a pathway. This can be applied to diverse organisms, calculating a similarity index based on shared KO id, gene position and protein-protein interactions. As an example of this tool, we demonstrate its application to the comparison of Bacillus cereus group of bacteria.