Example of segment swap in non-sequential alignment. Structures of glucokinase (PDB-code 1gc5:A) and 2-dehydro-3- deoxygluconokinase (PDB-code 1j5v:D) have been aligned by TOPOFIT with N
/RMSD of 234/1.7 Å. Alignment segments are colored in blue, magenta and orange. The right side of the picture displays the corresponding alignment plot. It is easy to see that if the orange and magenta segments would be swapped in either sequence of the compared proteins the result would be a perfect sequential alignment.