Positional P-values for multiple sequence alignments help revealing
structural changes in evolutionary related proteins:
Top: Manual alignment of fragments of human glyoxalase II (PDB ID 1qh5A) and bacterial
penicillinase (PDB ID 1sml). Strands b are shifted by one residue, so that structurally similar
residues correspond to different sequence positions. Bottom: structure alignment by DALI is
correct, but low positional P-values reveal contradiction to the sequence
similarity, as opposed to higher P-values for the profile-based alignment
of the two sequence families. β-strands a and b are shown as arrows, Zn-binding residues are boxed.