Fig. 1.

Region 4 of wild type σ⁷⁰ and mutant σ proteins and the T4 middle promoter P_uvsX. A. The C-terminal amino acid sequence of σ⁷⁰ is shown from residues 540 to 613. Residues in pink contact the -35 element of E. coli promoter DNA ⁸ while residues in blue contact the β-flap tip ¹¹; ¹²; ¹³; ⁴⁵. Every tenth residue is marked with a small vertical line. Above the sequence is shown the locations of regions 4.1 and 4.2 ¹ and the positions of the α-helices H1, H2, and H5 and the helix-turn-helix H3-T-H4 structures observed in region 4 of the primary σ of T. aquaticus complexed with -35 element DNA ⁸. Residues that contact AsiA in the AsiA/σ⁷⁰ region 4 structure ³⁰ are designated with an asterisk and the region of the MotA contact site ²⁰ is indicated. Below are shown the region 4 sequences of the mutant σ proteins, with residues that differ from σ⁷⁰ in red. B. The sequence of P_uvsX from −61 to +9 is shown with the start of transcription indicated as +1. The locations of the σ⁷⁰ –10 element and the MotA box are indicated. Sequences within P_uvsX that match the canonical polymerase elements σ⁷⁰ -10 element (TATAAT); σ⁷⁰ extended -10 element (-15T, -14G); σ⁷⁰ -35 element (TTGACA); and α UP element (AAAa/ta/tTa/tTTTTnnAAAA) are in red.