True biological non-sequential alignment in proteins with symmetrical structures. Structures of transaldolase B (PDB-code 1onr:A) and class I aldolase (PDB-code 1fba:A) have been aligned by TOPOFIT with Ne/RMSD of 142/1.8 Å. While the structures can be aligned in a sequential way, the best alignment found by TOPOFIT is a circular permutation. The alignment consists of two segments colored blue and green. The segment shown in green is located at C-terminal end in transaldolase, while in aldolase it is located at N-terminal end. The TOPOFIT alignment reflects the correct "biological" alignment as discussed in .