Question: Hypothetical protein in Prokka
0
gravatar for mauricio.morales
29 days ago by
mauricio.morales0 wrote:

Hi! What to do with the hypothetical protein in Prokka? Some program to improve this metric? Thank you!

prokka assembly genome • 133 views
ADD COMMENTlink modified 29 days ago by Mensur Dlakic6.9k • written 29 days ago by mauricio.morales0
1

You can use blastp to find similar proteins. Search for the conserved motifs in the protein using (cdd/pfam). Use GO information, pathways,..... depending on what you're looking for.

ADD REPLYlink written 29 days ago by Fatima630
1

You can use eggnog-mapper http://eggnog-mapper.embl.de/ to assign each protein an EggNOG orthology group, it's not being used with prokka.

ADD REPLYlink written 29 days ago by Asaf8.4k
1
gravatar for Mensur Dlakic
29 days ago by
Mensur Dlakic6.9k
USA
Mensur Dlakic6.9k wrote:

The exact number varies between genomes, but it is normal to have 1/4 to 1/3 of proteins annotated as hypothetical, uncharacterized or containing domains of unknown function. In fact, if you installed Prokka such that it uses Pfam, TIGRFams and COG/KOG databases, chances are that those ambiguous annotations will remain even after you try the databases suggested by other posters.

It is just how it is - for many proteins we still have no clues about their functions.

ADD COMMENTlink written 29 days ago by Mensur Dlakic6.9k
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