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Figure 3
Sequence-similarity scores calculated with various settings for an insertion in the model (PDB entry 2b9l ; Piao et al., 2005BB19). The target structure (PDB entry 1hj9 ; Leiros et al., 2001BB13) is shown in grey. Sequence similarity was calculated using (a) a high-precision structural alignment (target, HCY––––––––––KSGIQVR; model, HCVNSYQSNLDA­I––––KIR) using the binary scoring matrix and a null averaging window, or an FFAS alignment (target, HCYKS––––––GIQVR; model, HCV­NSYQSNLDAIKIR) and (b) the binary matrix and a null averaging window, (c) BLOSUM62 and a null averaging window or (d) BLOSUM62 and an averaging window of five. Blue indicates high sequence similarity, while red indicates areas in which sequence similarity is low. The figures were generated using MOLSCRIPT (Kraulis, 1991BB10) and were rendered with RASTER3D (Merritt & Bacon, 1997BB17).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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