Figure 5.

Structure of the pIP501 oriT region on DNA level. oriT region of pIP501 (nucleotides 1174–1420, GenBank L39769.1). Putative −10 and −35 promoter elements are colored in red; the TraN binding site is boxed. The perfect IR (IR1) is indicated with thick arrows; the second, imperfect IR (IR2) is marked with thin arrows—its repeating segments are individually named. Both repeats have the potential to generate a secondary structure. The areas that showed to be either protected from (gray box, mainly on the cleaved strand) or hypersensitive to (blue box, mainly on the non-cleaved strand) DNaseI cleavage in TraA footprinting assays (Kurenbach et al., 2006) are marked. oriT_pIP501 core sequence (GenBank L39769.1, bp 1259–1296) is indicated with a dashed box; oriT nic-site is shown by an orange vertical arrow. tra operon ribosomal binding site (RBS) is colored in blue; the start codon of the first tra gene (traA, TTG) is boxed and colored in green; a second, potential start codon (ATG) is marked with a dotted box.