Flavin transferase that catalyzes the transfer of the FMN moiety of FAD and its covalent binding to the hydroxyl group of a threonine residue in a target flavoprotein such as NqrB and NqrC, two subunits of the NQR complex. FAD + L-threonyl-[protein] = AMP + FMN-L-threonyl-[protein] + H(+) Inactivation of this gene results in a complete loss of the quinone reductase activity of the Na(+)-NQR complex, but does not affect the NADH dehydrogenase activity. Cytoplasmic fumarate reductase activity displayed by KPK_2907, which contains a covalently bound FMN, remains unchanged in mutant cells. Belongs to the ApbE family.