A real example of HSP found by PSI-BLAST. We define that MYSKILL (assuming that the window size is 7) is a similar peptide of MYKKILY and we treat it as an extended sequence feature of the query protein. The similarity level of MYSKILL and MYKKILY is 5 since there are five interchangeable residue pairs within that window. We can generate multiple similar peptides from protein gi|2622094 (Sbjct) for the query protein.
Lin et al. BMC Bioinformatics 2009 10(Suppl 15):S8 doi:10.1186/1471-2105-10-S15-S8