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 (By similarity). Displays FAD pyrophosphatase activity in vitro, hydrolyzing FAD into FMN and AMP (PubMed:23447540). FAD + L-threonyl-[protein] = AMP + FMN-L-threonyl-[protein] + H(+) Magnesium. Can also use manganese. Monomer. Belongs to the ApbE family.