Procedure to identify and extract domain boundary signals. To identify domain boundary signals for a target, homologous sequences are found using PSI-BLAST. The pairwise alignments generated by PSI-BLAST are used to form a multiple sequence alignment with the query sequence as the anchor. A domain boundary signal is defined as a gap which begins at the N or C terminal end of a sequence in the msa and extends continuously for at least 45 residues. With the gaps removed the remaining sequence must be at least 45 residues long for a signal to be generated. Here we see two domain boundary signals for 1B4A (location indicated by large arrows).