Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane. They are also involved in complex antagonistic ecological interactions between bacteria. We designed models and protein profiles to detect an unprecedented number and diversity (∼10000) of bacterial protein secretion systems (T1SS, T2SS, T3SS, T4SS, T5SS, T6SSi-iii, T9SS) and evolutionarily related appendages (T4P, Tad, Flagellum) in 1528 genomes of diderm bacteria.