Figure 3.

Example of a circular permutation in a non-sequential alignment. Structures of posphoinositide-specific phospholipase C delta (PDB-code 2isd:A, shown on a) and C2-domain of synaptotagmin I (PDB-code 1rsy, shown on b) have been aligned by TOPOFIT with the N_e/RMSD of 108/1.2 Å. The alignment consists of two segments colored in blue and green. The green segment represents a β-strand and is located at N-terminal in synaptotagmin and at C-terminal in phospholipase. Thus the alignment is the circular permutation. c) displays the circular diagram of the alignment. d) displays the alignment plot corresponding to the alignment.