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. Cannot use directly FMN instead of FAD as substrate. FAD + L-threonyl-[protein] = AMP + FMN-L-threonyl-[protein] + H(+) Belongs to the ApbE family. Extended N-terminus. Extended N-terminus.