Figure 1.

Example of a non-sequential alignment. Structures of hydroxynitrile lyase from Hevea brasiliensis (PDB-code 1yas:A, shown on a) and esterase from Alcaligenes sp. (PDB-code 1qlw:A, shown on b) have been aligned by TOPOFIT with N_e/RMSD of 175/1.7 Å. The corresponding alignment plot is shown on c), the connectivity of the aligned fragments is shown on d). The structural alignment consists of 7 fragments, which can be combined into 4 segments colored in cyan, blue, red and green. Three obvious cases of noise in the alignment are circled. A continuous line represents the longest sequential alignment and the non-sequential segment is termed NS. The figure also shows how the noise fragment termed z interferes with the two long fragments, x and y (grayed area).