Figure 4

Sequence features of Sigma-54 and its promoter. A) Functional architecture of the Sigma-54 sequence (adapted from [10]). The first HTH is responsible for recognition of the -12 element as was demonstrated by [61]. The solution structure of the C-terminal domain of Aquifex aeolicus Sigma-54 bound to the promoter implied that the RpoN box [173] and two flanking stretches interact directly with the -24 element of the promoter [174], confirming an earlier assertion of [175]. B) Sequence logo of the two HTH elements as present in all analyzed Sigma-54 proteins. The residue pairs whose substitution abolished binding activity in the elaborate Ala-Cys scanning mutagenesis study by [93], are marked by purple dots in-between. C) Reduced promoter sequence motif. The motif is based on the 85 promoters with validated transcription start site as collected by [14]. The position relative to the transcription start is given on the x-axis.