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. Surface residues mutate more easily than core residues. Core residues mutate easier when they make fewer contacts. It is hard to mutate a glycine that sits somewhere with torsion angles that other residues cannot have. We will now start working on sequence alignments.