Intragenic σ<sup>54</sup> ChIP-seq peaks.

<p><sup>a</sup> Unique ID; IS = Inside a gene in the Sense orientation, IA = Inside a gene in the Antisense orientation; each peak is assigned a unique number for cross-referencing with other datasets</p><p><sup>b</sup> Underlined text indicates that a σ<sup>54</sup> has been identified in the homologous position in <i>Salmonella</i> Typhimurium [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005552#pgen.1005552.ref014" target="_blank">14</a>]</p><p><sup>c</sup> Genome coordinate (U00096.2) of ChIP-seq peak center</p><p><sup>d</sup> FAT = Fold Above Threshold score (indication of ChIP-seq occupancy)</p><p><sup>e</sup> Associated motif identified using MEME; consensus positions indicated in bold</p><p><sup>f</sup> Genome coordinate (U00096.2) of motif center</p><p><sup>g</sup> Genomic orientation of associated motif</p><p><sup>h</sup> Overlapping gene</p><p><sup>i</sup> Genomic orientation of overlapping gene</p><p><sup>j</sup> Closest, appropriately oriented, downstream gene (from the predicted transcription start site, 19 bp downstream of the motif center), excluding the gene that the binding site is within</p><p><sup>k</sup> Distance from the predicted transcription start site (19 bp downstream of the motif center) to the start of the closest, appropriately oriented, downstream gene (bp)</p><p><sup>l</sup> Position Specific Scoring Matrix (PSSM) score (indication of similarity to the consensus site; see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005552#sec018" target="_blank">Methods</a>)</p><p>Intragenic σ<sup>54</sup> ChIP-seq peaks.</p>