Exercise 2: Sequence Conservation

Before beginning this exercise, change the highlighting style back to Bonds and the Molecule Coloring to Sequence Identity per residue. In order to display sequence conservation, follow these steps.

1 Go back to the main MultiSeq window top pull-down menu and select Tools $\rightarrow$ Residue Selection. 2 Select Sequence Identity. 3 In the Sequence Identity window, set the measure to Greater than. 4 Select the value 0.5. 5 Click the Select button.

Figure 15: Exercise 2

 
Do you notice a difference in the highlighted areas, in comparing the structure (Q) to sequence? Upon examining the residues in the Sequence display, notice how the majority of the sequence conservation occurs among the top 3 molecules. Since the top 3 molecules are AspRS and the bottom is SerRS, this pattern of sequence conservation makes sense.
 
Go back to the Sequence Identity window. Decrease the value to 0.2 and click Select. Take note of how many conserved residues are in the OpenGL Display and Sequence Display. Now, increase the value back to 0.5. You will see, as you progress, the yellow color diminishing among the molecules.

Figure 16: Sequence Identity$\ge$0.7

 
The yellow coloring remains towards the core of the molecule and at the dimerization site. Increase the value to 0.7 and click Select; you should notice that the only highlighted sequences in the Sequence Display are those that match exactly. Finally, change the value to 1.0. Between Sequence Identity $\ge$0.7 and Sequence Identity $\ge$1.0, there are only 10 residues which are identical and span all four molecules. Go back to the Sequence Identity window and click on the Close Window button.

Figure 17: Highlighted residues in Sequence Display