Objective

To perform a pairwise sequence alignment between rhodopsin and a GPCR sequence.

Background

Here you will become familiar with sequence manipulation and pairwise alignment.

Instructions

1. Read the PDB structure 1F88
2. File/Load/Swissprot and enter 5HT1A_Human (human serotonin GPCR).
3. Now we need to extract the sequence data from subunit a of 1F88. Right click on the 1F88 subunit .a. and select the .Extract Sequences. option..
4. Double click on one of the sequences in the ICM workspace (using the ALL tab), hold down the Ctrl key and click on the other . both sequences should now be highlighted in blue.
5. Right click on them and select Align Sequences. The alignment should be displayed in the alignment editor.
6. Check the box under the heading .Show secondary structure for. in the ICM Alignment Editor. You may have to scroll down to see this option). The secondary structure of 1f88 is then shown in the alignment.

Manual References (Web Links)

How to Align Two Sequences

Alignment Editor