Searching for common sequence patterns among distantly related proteins

We have developed a program Gap Allowing Pattern Explorer (GAPE)to extract amino acid sequence motifs conserved among distantlyrelated proteins. The GAPE program is designed to allow gapsin the sequences. First, this program generates all possibleamino acid patterns comprising up to five amino acids. Sequencescontaining the amino acid residues in the same order as a generatedpattern are selected as subsequences, where the differencesin the distances between two consecutive amino acids are ignored.Next, the motifs are extracted from the subsequences under conditionsin which all four distances between the five amino acids arefixed. At this stage, motifs with gaps in their subsequenceare also found by relaxing one of the four fixed distances.The statistical significance for a motif obtained is calculatedbased on the amino acid composition of the sequences under consideration.When the GAPE program was applied to 59 pyridoxal-phosphaterelatedsequences and 64 ATP (AMP-forming)-related sequences, motifsextracted with a low expectation of occurrence contained someof the amino acid residues chemically proved to be involvedin the ligand recognition.