Intergenic σ54 ChIP-seq peaks.

a Unique ID; OS = Outside of a gene in the Sense orientation, OA = Outside of a gene in the Antisense orientation; each peak is assigned a unique number for cross-referencing with other datasetsb Underlined text indicates that a σ54 has been identified in the homologous position in Salmonella Typhimurium [14]c Genome coordinate (U00096.2) of ChIP-seq peak centerd FAT = Fold Above Threshold score (indication of ChIP-seq occupancy)e Associated motif identified using MEME; consensus positions indicated in boldf Genome coordinate (U00096.2) of motif centerg Genomic orientation of associated motifh Closest, appropriately oriented, downstream gene (from the predicted transcription start site, 19 bp downstream of the motif center)i 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); note that for OS07, the ChIP-seq peak is intergenic but the predicted transcription start site is intragenicj Position Specific Scoring Matrix (PSSM) score (indication of similarity to the consensus site; see Methods)k P = Promoter is Predicted in Ecocyc; C = promoter is experimentally Confirmed in Ecocyc [26]Intergenic σ54 ChIP-seq peaks.