We align our protein against a series of family members that have been purified from thermostable bacteria. We look at the multiple sequence alignment, and if we see positions where all the stable proteins have the one residue, and the not so stable ones another, we have a beginning. A third example will pop up in due time. So lets align sequences. Nevertheless, I think that this alignment is the best that can be achieved for these two sequences.
Lets think about an alignment.
An alignment is a representation of a whole series of events that took place during evolution and that left their traces in the sequence. Once nature decided on an indel, its length is less important, but longer indels are more difficult to make than shorter ones. Active site residues don't mutate. Residues mutate more easily to residues encoded by similar codons. Cysteines that sit in cysteine bridges don't mutate easily.