Mikita Suyama (suyama@kuicr.kyoto-u.ac.jp)
Takaaki Nishioka (nishioka@kuicr.kyoto-u.ac.jp)
Jun'ichi Oda
Institute for Chemical Research,
Kyoto University
Uji, Kyoto 611, Japan
We have developed a program GAPE (Gap Allowing Pattern Explorer) to extract amino acid sequence motifs conserved among distantly related proteins. The GAPE program is designed to allow a gap in the sequences. When the program is applied to some ligand-related consensus sequences, motifs extracted with low expectation of occurrence contain some of the amino acid residues chemically proved to be involved in the ligand recognition.