We have developed a pattern comparative method for identifying functionally important motifs in protein sequences. The essence of most standard pattern comparative methods is a comparison of patterns occurring in different sequences using an optimized weight matrix. In contrast, our approach is based on a measure of similarity among all the candidate motifs within the same sequence. This method may prove to be particularly efficient for proteins encoding the same biochemical function, but with different primary sequences, and when tertiary structure information from one or more sequences is available. We have applied this method to a special class of zinc-binding enzymes known as endopeptidases.