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After folding, the 3-dimensional allignment of the three active regions
may be the same. Though these two proteins should have a good BLAST
score and would be placed in the same family, the results will not
suggest that there is an acient evolutionary relationship between
them and than one was generated from the other by a translocation of
region A.
Sasha Gorbalenya found such a condition. He and I worked on a procedure
to check four proteins from the same family. We found that two of them had
such a relationship, though the other two did not. Others involved
in this study examined the related proteins and found them to have the
same structural orientation of important residues.
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