Hi all! I am doing homology modeling for a transmembrane protein (sodium channel). I am still in the phase of aligning the sequences (query and template(s)). To better determine the sub-cellular location of the different segments and to improve the quality of the alignment, I have to do a multiple sequence alignment. My advisor was very vague and I am new to all of this. I saw that in many different studies this is a common thing to do (many papers with the picture of the MSA highlighting the conserved regions etc...). Nevertheless, I found no tutorial explaining how to do this. I only know that I need many sequences that I should then align to find the conserved regions. How do I find all these sequences? Can I use Blast? At the moment I used it to find my template (homologous) using PDB in the option (since I need a structure). Is it a good idea to find the sequences of the members of the sodium channel family (SCNxA, x = 1:11) of human and other species and then align them? Do I have to bother myself with the value of identity or not for this phase?
Thanks a lot.