Fig. 4.

NtcA-activated and -repressed promoters. (A) Promoter regions of 20 TSS (underlined nucleotide) in the DEF⁺ category with the highest fold change. Possible −10 elements are highlighted in blue, nucleotides matching the consensus for NtcA binding sites in red. (B) Nucleotide frequencies derived for positions 1–14 of 87 putative NtcA binding sites. (C) Corresponding Weblogo. (D) Position of NtcA binding sites identified in a sliding window approach using the PSSM along the promoters in the DEF⁺ category (fold change ≥8). The bars indicate the first nucleotide of a putative NtcA binding site and its position with regard to the TSS (E) Putative NtcA binding sites identified at repression-compatible positions around TSS in the DEF⁻ category.