Catalyzes the 6-electron oxidation of protoporphyrinogen IX to form protoporphyrin IX; under anaerobic conditions uses menaquinone as an electron acceptor, under aerobic condition uses ubiquinone as an electron acceptor. 3 a menaquinone + protoporphyrinogen IX = 3 a menaquinol + protoporphyrin IX 3 a ubiquinone + protoporphyrinogen IX = 3 a ubiquinol + protoporphyrin IX 3 a quinone + protoporphyrinogen IX = 3 a quinol + protoporphyrin IX Binds 1 FMN non-covalently per subunit. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrin-IX from protoporphyrinogen-IX: step 1/1. Belongs to the HemG family.