Can someone explain me why there are two eggNOG 4.5 databases for Bacteria? There is the precomputed HMM database for bactNOG and bact_50 available here: http://eggnogdb.embl.de/download/eggnog_4.5/hmmdb_levels/
the databases bact_50 and bactNOG are not exactly the same. The first (bact_50) includes all bactNOG groups plus all OGs in children taxonomic levels for bactNOGs including more than 50 sequences (this is to increase HMM resolution in groups that are too large). Something similar occurs with euk vs eukNOG and arch.