Few things need to be considered while selecting your templates. And the selection completely depends on the aim of the project. If you are planning to model full length sequence of your(target) sequence, sequence identity and sequence similarity as well as query coverage matter a lot. On the other hand, if you want to look only the catalytically/functionally important sites/regions, templates with lower sequence identity might also help a lot because it has been shown that in most of the cases functionally important residues are conserved among related proteins.
Of course you can also use multiple templates if they have similar folds or belong to the same family. Also, the first hit provided by blast search might not always be the most appropriate template. Because sometimes, such templates although contain higher sequence identy, may correspond only part of the query sequence (sequence you want to model). So look at the query coverage also along with sequence identity.
Okay in your case, you could use the first template if you do not want to use multiple templates. However, I would recommend you to go through the UniProt entry for this protein sequence (http://www.uniprot.org/uniprot/q9bxm7) in detail before you proceed with modeling. In fact, UniProt provides wealth of information regarding protein sequences and you might get some of your answers from there. You can also find homology based models for this protein already been deposited. And if you are satisfied, you can use the models available there.
I hope this helps a bit in your understanding. And tell me if you are confused with anything written by me or do not understand some points.
modified 9.7 years ago
9.7 years ago by
Pals • 1.3k