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Figure 3 | BMC Bioinformatics

Figure 3

From: AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Figure 3

Examples of two pairs of proteins with structural similarity between profiles that can be considered as false positives according to SCOP definition. A) two proteins belonging to two different SCOP folds. The similarity in structure is evident from the figure and is also noted in the SCOP database. The structure on the right is 1KU9, N terminal part and the structure on left is 1BM8 (winged helix domain). The inset shows the full length proteins and the foreground picture shows the superposition of the part of each protein suggested to be homologous by AlignHUSH. B) two proteins belonging to different SCOP folds in the same class. Visual inspection does not seem to bring out the similarity between the two proteins and perhaps this is the reason why they are classified into two different folds by SCOP. The DALI Z score between the two proteins is around 8.0 covering 150 residues with an RMSD of 3.3 Å.

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