Hi all. With the final goal of building a homology model of a sodium channel I identified the best template. Nevertheless, the alignment is not very good and I have been advised to perform a multiple sequence alignment (MSA) with the orthologous of this protein. This, should give me information about the sub-cellular location of the different segments (helices, intracellular etc...) and should guide me in the manual modification of the alignment with the template. The problem is that I do not know how can a MSA with other sodium channels (MSA that does NOT contain the template I will use for the model) help me in this. I have been looking for some notes or tutorials but I found nothing. Any help is appreciated.
- EDIT * Is it possible that if, for example, from the MSA with the homologous sequences (no template) I see that there is a long portion that is highly conserved, then I must keep it in the alignment with the template (no gaps in this region)?