FIG 4.

Phage 7-11–ECF28 subgroup σ factor alignment. (Top) Multiple alignment of the phage 7-11 σ factor (boxed in green) and selected representatives of the ECF28 subgroup. The segment of the alignment that is shown corresponds to the C-terminal part of the σ₂ domain (with the vertical line indicating the C terminus) and the sequences C-terminal of the indicated σ₂ domain boundary. The shaded area in the alignment corresponds to the segment implicated in interacting with the −10 element extension in the promoter recognized by phage 7-11 σ factor. Below the alignment is the sequence logo of that promoter, with the −10 element extension shaded and the coordinates shown relative to the transcription start site. (Bottom) Multiple alignment of the entire ECF28 subgroup. The conserved segment interacting with the −10 element extension is shaded. Below the alignment is the sequence logo of the shaded segment, together with the C-terminal flanking sequences that reach down to the first gap in the multiple alignment.