Hypothetical protein in Prokka

Question

[mauricio.1313]

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

[Fatima]

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.

[Asaf]

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.

Answer 1

[Mensur Dlakic]

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.