Sequence features of Sigma-54 and its promoter. A) Functional architecture of the Sigma-54 sequence (adapted from ). The first HTH is responsible for recognition of the -12 element as was demonstrated by . The solution structure of the C-terminal domain of Aquifex aeolicus Sigma-54 bound to the promoter implied that the RpoN box  and two flanking stretches interact directly with the -24 element of the promoter , confirming an earlier assertion of . 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 , 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 . The position relative to the transcription start is given on the x-axis.