Table 1.
DNA-amino acid contacts in FadR from E.coli and AraR from B. subtilis.
Table 2.
General statistics of the analyzed GNTR-family TFs.
Fig 1.
Heat map of correlations between amino acids and nucleotides for FadR-subfamily TFs and their binding sites.
Sequence logos of HTH DNA-binding domains and corresponding binding sites are shown on the top and to the left of the heat map, respectively. The total height of the symbols in each position equals the positional information content, whereas the height of individual symbols is proportional to the positional amino acid or nucleotide frequency. The correlation scores are color ramped from yellow to red for amino acid-nucleotide pairs with statistical significance greater than an automatically defined threshold (with red assigned for the most correlated pair). The violet-black palette is used for other pairs.
Fig 2.
Heat map of correlations between amino acids and nucleotides for HutC-subfamily TFs and their binding sites.
Notation as in Fig 1.
Fig 3.
Heat map of correlations between amino acids and nucleotides for YtrA-subfamily TFs and their binding sites.
Notation as in Fig 1.
Table 3.
Interdependence of the intergenic distance and the distance to a single site.
Fig 4.
Distances between regulated genes and TF-binding sites in divergons with single sites.
A—operons with a TF gene; B—operons with structural genes only; C—the control group (includes divergons without TF genes). The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Each dot corresponds to one site. The regression lines are shown. Blue color denotes the FadR subfamily; red color, the HutC subfamily.
Table 4.
Two fractions of divergons with double sites, interdependence of the intergenic distance and the distance between double sites.
Table 5.
Interdependence of the intergenic distance and the distance to the proximal TF-binding site in divergons with common double sites.
Fig 5.
Distances between double sites in divergons.
A—divergons with a TF gene; B—the control group. The vertical axis is the inter-site distance. The horizontal axis is the intergenic distance. Notation as in Fig 4.
Fig 6.
Two groups of divergons with double sites.
A—the first group (constant inter-site distance); B—the second group (increasing inter-site distance). For details, see the text. The vertical axis is the inter-site distance. The horizontal axis is the intergenic distance. Notation as in Fig 4.
Fig 7.
Distances between regulated genes and proximal TF-binding sites in divergons with common double sites.
A—operons with a TF gene; B—operons with structural genes only. The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Notation as in Fig 4.
Table 6.
Interdependence of the intergenic distance and the distance to the proximal TF-binding site in divergons with separate double sites.
Fig 8.
Distances between regulated genes and proximal TF-binding sites in divergons with separate double sites.
A—operons with a TF gene; B—operons with structural genes only; C—the control group. The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Notation as in Fig 4.
Fig 9.
Positioning of additional boxes and control pseudoboxes.
True binding half-sites are shown in blue; additional boxes, in violet; pseudoboxes, in red arrows. For details, see the text.
Fig 10.
Distribution of Snear and Srandom in the FadR, HutC and YtrA subfamilies.
The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes Snear values; red color—Srandom values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.