I have a template i.e. transcription factors protein my aim is to predict 3D structure of that protein. I am using PSI-BLAST for target search, but in PSI-BLAST, similarity is showing NADPH-dependent oxidoreductase protein. So my doubt is can i take this protein as a target for further study. (Modelling) ?
No - while orthologous proteins in closely related organisms usually are more highly conserved than paralogous proteins with divergent functions, homology models can be produced from structures with divergent function, as long as the domain fold is sufficiently conserved. The main thing to look for in the alignment of potential template is a reasonable homology along the full length of the domain, not just high similarity of a limited subsequence. In addition, if you color the sequence differences between your query sequence and the potential templates on the structure of the template, you want to see non-conservative substitutions mainly on the surface, while core substitutions should be much rarer and more conservative. In particular, you expect structurally very relevant residue types such as Gly, Pro, Trp and, for extracellular Proteins, Cys to be highly conserved.
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