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I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using HHpred.

So far, I have done the following:

  • obtained FASTA sequence and inputted it into HHpred.
  • Loaded the FASTA sequence on to HHpred.

What I am looking to do on HHpred now:

  • Identify the different domains/motifs of this uncharacterized protein
  • Compare full length protein to two separate domains
  • Determine if the predictions has improved by comparing the full length proteins to the separate domains.

All comments help, I am very desperate for any tips.

Thank you!

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  • $\begingroup$ Do the automated annotation databases, such as PFam etc., in the Uniprot section Family & Domain, have anything annotated? Are they missing the domain you are after (they generally do), is the boundary wrong (they generally are), do you want more granularity (family too big) etc, etc? $\endgroup$
    – Matteo Ferla
    Feb 1, 2022 at 17:12

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