Catalyzes the reduction of FMN to FMNH2 which is used to reduce pyrimidine by RutA via the Rut pathway. In vitro, the flavin reductase Fre can substitute for the function of RutF, however, RutF is required for uracil utilization in vivo. FMNH2 + NAD(+) = FMN + 2 H(+) + NADH Up-regulated by the nitrogen regulatory protein C (NtrC also called GlnG) and repressed by RutR. Cells lacking this gene fail to grow on uridine as the sole source of nitrogen at room temperature. The Rut pathway degrades exogenous pyrimidines as the sole nitrogen source at room temperature but not at 37 degrees Celsius, a restriction that is apparently a consequence of an inadequate ability to remove toxic malonic semialdehyde at the higher temperature (RutE/YdfG function). Belongs to the non-flavoprotein flavin reductase family. RutF subfamily.