What database does prokka use for comparison by default?
Welcome, @Angela_Barrios
Prokka in Galaxy works the same as using the tool directly.
You can see the annotations applied on the web form here. If everything is at default, then “Bacteria” is applied.
More details: GitHub - tseemann/prokka: ⚡ Rapid prokaryotic genome annotation
Galaxy GTN Tutorials: Galaxy Training!
Hope this helps! 
There is also bakta that you can try. It is the successor for prokka for many use-cases.
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