I've seen common conjugation systems use RP4, R388, R1, F plasmid, etc but which system is most related across every conjugation system? Which proteins are found in most/all of the conjugation systems?
The conjugation system belongs to the plasmid, not to the host. So asking which is conserved across the most species doesn't really make sense. If you want to be more precise about what you are asking, there might be someone who can answer.