Fig. 3

Example of a simple but significant structural re-arrangement. Structure superposition of the putative oxidoreductase from Pseudomonas putida (the query; PDB code 3L6D, chain A) and the human Cytokine-like Nuclear Factor N-Pac (the target; PDB code 2UYY, chain A) generated with MOMA. The conserved domains are shown in the alignment and the sub-matrices remarked by grey and red blocks (Top Panel). The two structures are rainbow colored (Bottom Left) and the resulting SSE pairs aligned are shown in red and orange colours (Bottom Middle). The alignment of SSE elements is also represented with aligned blocks highlighted (Bottom Right). Each superposition was carried out with different rotation matrices and translation vectors. In this example MOMA was executed with the following parameters: g1 = −4, g2 = −4 and C = 45