I have been involved in modeling proteins that have initial %identity of 22, 26 and 23. I tried to imply a couple of strategies.
I filtered the homologous sequences that are only related to my model sequence, made MSA and combined with the MSA that was made with homologous sequences of the used template.
I used the mixture of non-redundant protein sequences of both template and target (50/50) and then made structure based sequence alignment using 3D-COFFEE.
I made MSA of model sequence using NR-sequences derived from BLAST and another MSA of template derived from secondary structure prediction method (JPRED). I combined those two MSAs to make final MSA.
However, I am not satisfied with any of the above strategies. The thing is that the ligand-substrate binding site is almost conserved with any of the methods but the overall structure always worse.
I am using discovery studio for making sequence alignment that uses modified CLUSTAL W algorithm.Model building is a never ending process and when the sequence identity is below 30%, there is always a problem. However, I still want to improve the alignment so it would be a great help if anyone can suggest me the fourth approach that would benefit my problem.
Thanking you in advance!!