Protein Sequence

Now that we have examined the structural conservation between the molecules, it is important to examine the sequence conservation. Sequence conservation occurs when amino acid identity of the aligned residues match.
In order to access Sequence Identity per residue:

1 Click on the View menu.

2 Select Molecule Coloring $\rightarrow$ Sequence Identity per residue.

Figure 9: Sequence Identity per residue

 
Now take a look at the OpenGL Display window. As you can see, the majority of the aligned molecules have turned red. Notice that only 10 residues are strictly conserved (blue), and these areas are important for catalysis and dimerization.

Figure 10: Sequence Conservation

 


The coloring of the molecules using Sequence Identity per residue indicates that the sequence conservation is much less in comparison to the structural conservation. This may be difficult to see right now. However, in Residue Selection sequence conservation is easier to observe, using the Sequence Display.

 


To examine the relationship between sequence and structure in more detail, we will use the Residue Selection feature.