The extended consensus CDX1-binding sequence, according to the TRANSFAC database, is also shown.
Two motif finding programs, MEME [ 25, 43] and BioProspector [ 26], were then applied to these pooled inter-TU regions to identify palindromic 14-mers as putative LexA-binding sites in these sequences according to previous studies [ 16].
To this end, we divided the 5897 possible AbrB-binding sequences into 20 sets each containing 300 sequences, according to average AbrB-binding signal intensities (Supplementary Table S2 and Supplementary Fig. S4C), and the consensus sequence for each set was extracted by the Bipad program (Fig. 5).
Regarding molecular functions, binding (44.95%) was the most represented sequences according to GO terms, followed by catalytic activity (33.79%).
The program scores the input sequences according to fit with the loose consensus sequences; scores above a default threshold value are predicted to act as SR protein binding sites and thus function as ESEs.
Unspecific binding is monitored by competition with an oligonucleotide containing the consensus PPAR γ response element sequence, according to the manufacturer's protocol.
Bacterial CDOs show low overall similarity with eukaryotic CDO (12 21% identity with rat CDO) but have a conserved 3-His metal binding site, according to sequence alignments.
The experimental results indicated that the investigated complexes could bind to DNA via intercalative mode and showed a different DNA binding activity according to the sequence: bsari > bshi > bsali > bsasi > bsphali.
To substantiate this finding, we clustered binding sites according to their sequence similarity and compared them to a compendium of other, previously published ChIP-sequencing data sets.
Six genes namely hrpG, pcaQ, blal, XAC3026, XAC3445, and XAC3446 were known to have sequence specific DNA binding activity according to GO annotation.
