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(+) Homodimer. Cells lacking this gene are conditional thiamine auxotrophs, and display phenotypic behaviors similar to those of strains lacking isc (iron-sulfur [Fe-S] cluster biosynthesis) operon functions. Belongs to the ApbE family. Was originally thought to be involved in synthesis of the pyrimidine moiety of thiamine and/or in metabolism of Fe-S clusters.