Tools for predicting protein function?

Question

[jamie.pike]

I am trying to gain insight into the potential function of a list of candidate effector protein sequences I have identified. I have searched using NCBI BLASTP against the nr database, performed GO analysis, searched for known domains using InterProScan and blasted them against the PHI-Base database, but still, the majority are annotated as “hypothetical proteins” and have no known protein domains.

I am struggling to decide where to go next to try to gain insight into their potential function. I have considered trying to predict the 3d structure, but I would have to do this for 72 sequences and then what? I can’t find a database to search protein structures against.

Does anyone have any suggestions where to go next? Are there other papers, tools, or approaches you could suggest to gain more insight into potential function?

Thanks,
Jamie

[jgreener]

Regarding the 3D structures, you could predict the structures and scan them back against the PDB with mTM-align. Then look at the functions of any close hits. You will need decent length sequence alignments though.

Answer 1

[Mensur Dlakic]

Though unlikely, it is possible that all your proteins are uncharacterized and have no known domains. It is possible that some of them are not proteins at all. You may want to try the links below if you haven't already done so.

• https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
• https://pfam.xfam.org/
• http://smart.embl-heidelberg.de/
• https://toolkit.tuebingen.mpg.de/tools/hhpred

[Dunois]

hhsuite might be a good option at this point.. There's also a new Pfam-N available which might be worth a try.