TFB and TBP binding to DNA in Archaea. (A) Illustration of coordinated binding of TBP/TFB to form a transcription initiation complex on DNA. Note significant bending of DNA around bound TBP/TFB complex. (B) Reproduction of P. furiosus gdh promoter sequence (top) compared to logo alignment of MotifCatcher-derived motif (bottom). In the gdh promoter sequence, shading indicates the TATA box and BRE elements and a black rectangle indicates the transcription-bubble region. Positions above the sequence are relative to the TSS, and arrows indicate phosphates analyzed in. The logo motif was formed by aligning sequences near 223 of the 417 (53%) reported TfbB, TfbD, and TfbG ChIP-seq peaks. Conserved elements between the gdh promoter and MotifCatcher-derived motif are indicated by green boxes surrounding the gdh promoter elements and by black lines extending vertically from the motif to gdh promoter sequence. The putative BRE, TATA box, PPE, and TSS in the logo are indicated with colored rectangles (red and green, BRE; white, TATA box; PPE, black; TSS, vertical white), and text annotation. An axis under the motif displays the most commonly discovered distance of sequence elements relative to the closest TSS in the Hb. NRC-1 genome. The distance of elements from the Hb. NRC-1 motif logo and elements in the P. furiosus gdh promoter to their respective TSS matched precisely.