Comprehensive analysis of σ⁵⁴ promoter motifs in P. putida. (A) Distribution of motifs in a 40-bp stretch of ARES mapped with RNA. (B–E) Sequence logos representing the refined σ⁵⁴-specific −12 and −24 promoter motifs, derived from an extensive analysis of 64 966 unique DNA templates. (F) Frequency analysis of nucleotide occurrences at the σ⁵⁴ TSS in P. putida. (G) Graphical representation of the RNA read distribution across the ARES in the library. (H) Distribution of motifs in a 40-bp stretch in the most highly transcribed ARES (top 15%) within the library. (I, J) Two pair of −12 and −24 motifs identified in the high-expressing group. (K) Frequency of nucleotides at their TSS.