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Figure 4
Sequence-similarity scores calculated with various settings for a deletion in the model (PDB entry 1hj9 ). The target structure (PDB entry 2b9l ) is shown in grey. Alignments are identical to those used for Fig. 3[link], but the roles of target and model are reversed. Sequence similarity was calculated using (a) a high-precision structural alignment using the binary scoring matrix and a null averaging window, or an FFAS alignment and (b) the binary matrix with 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 rendered with RASTER3D (Merritt & Bacon, 1997BB17).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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