Although the DALI server gives you sequence fragments that are similar in structure to your model, DDMP provides a visual representation of which regions are similar in structure.
The image below shows a portion of the output of a DDMP comparison between the pyrococcus woesei TATA-binding protein and the similar saccharomyces cerevisiae TATA-binding protein:
Those areas that are essentially white represent regions of close structural similarity. The colors are interpreted to mean that residues 47 -57 of the pyrococcus woesei protein (in red) are closer to the center of mass than the corresponding residues (~79 -89) of the saccharomyces cerevisiae protein. In contrast residues 34 -41 of the pyrococcus woesei protein (in blue) are farther away from the center of mass than the corresponding residues in the yeast protein.
This difference can be easily seen in the following superpositioning of the two chains. The red and blue regions correspond to the two pyrococcus woesei regions just mentioned:
Frequently the DDMP comparison will point out similarities and differences not easily seen in a molecular graphics display or in lists of sequence fragments.
Back to Post-structure Analysis
Revised: Tuesday, 20-Oct-1998 14:49:23 EDT