How can a MSA be useful for sub-cellular location identification?

Question

[fabbrl]

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.

Lorenzo

• 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)?

Answer 1

[ALchEmiXt]

I think what they mean is looking for orthologs or orthologous domains for which pdb templates could be available. You could use those domains for homology modelling... The MSA will help you to identify those regions of interest.

[fabbrl]

No, I already have the template. I have been asked to perform a MSA with other sequences (other members of the family).

[ALchEmiXt]

ok. Then the MSA might help you using those domains to predict which region of you protein might be located intracellular, in memberane or exposed.... this annotation has to be known though for the ortologous domains. Alternatively use some of the subcellular localization tools out there.