The common-use gap penalty strategies, constant penalty and affine gap penalty, have been adopted in the traditional three-sequence alignment algorithm which considers the insertion, deletion, and substitution.??However, these strategies are not suitable to protein sequence alignments.??For the alignment accuracy of protein sequences, the gap penalty is a major determinant.??Incorporating protein structure information to vary the gap penalties can lead to more biologically correct alignments.??Here, we present an algorithm to find a global and optimal alignment among three protein sequences by using position-specific gap penalties which allow gap penalties to be varied.??Thus, residue-dependent information and protein structure information can be applied to the three-sequence alignment.??The experimental results show that our algorithm achieves the significant improvement in the accuracy of alignments than the three-sequence alignment algorithm with the affine gap penalty for protein sequences.