My understanding: Prodigal will by default use translation table 11. It tries to detect codon usage and may switch to table 4 automatically. You should see a warning if the tool cannot make sense of the input with either. As far as i know there is no autodetection for other tables. You can use the argument -g 25 to specify table 25 manually. I don't know a prodigal-only solution for when your Gracilibacteria are part of a metagenome, though. You would have to do some taxonomic binning first (which is recommended before prodigal usage anyways).