Nonconsensus sites are recognized by the Bcd homeodomain but not the Ftz(Q50K) homeodomain. Shown are gel shift assay results of either recombinant homeodomains (A) or in vitro-translated full-length proteins (B) on three different types of Bcd sites. A1 contains a consensus sequence, TAATCC; X1 and X3s contain nonconsensus sequences, TAAGCT and TGATCC, respectively. For the experiments shown in panel A, the proteins used were none (lanes 1, 4, and 7), the Bcd homeodomain (lanes 2, 5, and 8), and the Ftz(Q50K) homeodomain (lanes 3, 6, and 9). For the experiments shown in panel B, the proteins used were none (lanes 1, 6, and 11), control lysate with luciferase translated (lanes 2, 7, and 12), lysate containing LexA-Bcd (lanes 3, 8, and 13), lysate containing LexA-Ftz(Q50K) (lanes 4, 9, and 14), and lysate containing LexA-Bcd-Ftz(Q50K)HD (lanes 5, 10, and 15). (C) Full-length proteins generated in an in vitro translation system. Lanes 1 to 3, LexA-Bcd, LexA-Ftz(Q50K), and LexA-Bcd-Ftz(Q50K)HD, respectively. See Materials and Methods for further details.