How higher quallity annotations can we expect?

[Rob-murphys]

Firstly thank you for making an awesome tool that I love using for its easy of use and what I believe to be good annotations.

I recently came across this post on Biostars by Mensur Dlakic, who from my time on the site seems to know his stuff, saying:

prokka comes only with HAMAP database of HMMs, which will produce terrible annotations on prokaryotic genomes

He goes on to say we should use the Pfam and TIGRfams database, which i guess we can do through prokka by adding them to the Prokkas hmm directory.

But my question is, why would this have been posted and is there any truth to it that we will get better annotations using different databases?

Best Lamma