Figure 2
From: Identifying promoter features of co-regulated genes with similar network motifs
PhoP-regulated promoters are described on the basis of five types of features. We conform a database including whether the position of the PhoP box suggests that a promoter is activated or repressed (activated/repressed); the orientation of the PhoP box (orientation); distinct PhoP box patterns (motif patterns); the distance of the PhoP box relative to the RNA polymerase site and the class of sigma 70 promoter (RNA polymerase sites); and the presence of potential binding sites for 24 transcription factors in the PhoP-regulated promoters (Other TFBs). The identification of a feature in a promoter is based on measuring the degree of match between a promoter instance and a model that represents that feature, which results in a vector of [0, 1] values where 1 (red) corresponds to maximum matching and 0 (green) corresponds to the absence of the feature. Individual genes are allowed to have more than one promoter because more than one candidate PhoP box can be identified in an intergenic region. In addition, promoters for the same gene in different genomes are considered separately in the E. coli and Salmonella genomes. Activated/repressed analysis discriminates among three groups (A1-A2) corresponding to activated, and repressed genes, respectively. The PhoP box could be present in the opposite (O1) or the same (O2) orientation as the regulated open reading frame. Pattern analysis of the PhoP box resulted in four preliminary groups (M1-M4). RNA polymerase sites analysis revealed six groups (P1-P6) corresponding to types and location of sigma 70 promoters: (1) close class II, (2) close class I, (3) medium class II, (4) medium class I, (5) remote class II and (6) remote class I. The presence of other transcription factor binding sites in PhoP-regulated promoters includes: (1) OxyR, (2) FruR, (3) DeoR, (4) MalT, (5) MelR, (6) CytR, (7) GlpR, (8) ArcA, (9) FNR, (10) RcsB, (11) Fur, (12) ArgR, (13) RhaS, (14) AraC, (15) CRP, (16) DnaA, (17) YhiW, (18) Lrp, (19) NarL, (20) FIS, (21) IHF, (22) OmpR, (23) PmrA and (24) SlyA.