>Sigma factors
>5|P06134|ADA regulatory protein (Regulatory protein of adaptative response) [Contains: Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (O-6-methylguanine-DNA alkyltransferase)]|Escherichia coli|AraC
In the absence of methylated Ada, RNA polymerase can bind at the -60 and -40 region of ada and aidB promoters via its alpha-CTD, but it fails to establish strong interactions with the core promoter. Methylated Ada does not recruit RNA polymerase to the ada and aidB promoters. Instead, upon binding of alpha to the UP element, methylated Ada interacts with a negatively-charged patch of sigma 70 CTD activating transcription.
The Ada protein also interacts with sigma 70 CTD at the alkA promoter but in this case Ada interacts with a positively-charged patch.
>15|P03021|Arabinose operon regulatory protein|Escherichia coli O157:H7|AraC
The binding site of AraC at ParaBAD overlaps the RNA polymerase -35 recognition region by 4 bases. Despite the overlap, sigma does read DNA in the -35 region. Since sigma and AraC are thus closely positioned at ParaBAD, it is possible that AraC and sigma contact one another during transcription initiation.
At ParaBAD it is likely that the C-terminal domain of the alpha subunit of polymerase interacts both with CRP and with AraC.
>44|Q9ZFU7|HTH-type transcriptional regulator eutR (Ethanolamine operon regulatory protein)|Salmonella typhimurium|AraC
A good potential sigma 70-binding site was found 83 nucleotides before the start of the eutS gene.
>47|Q47129|Transcriptional activator feaR|Escherichia coli|AraC
A consensus sequence for cyclic-AMP receptor protein binding is adjacent to the putative promoter for the maoB gene.
>97|Q05587|Regulatory protein pocR|Salmonella typhimurium|AraC
Probable interaction with sigma 70 subunit.
>108|P09378|L-rhamnose operon transcriptional activator rhaR|Escherichia coli|AraC
DNA-contacting residues in RNA polymerase alpha-subunit C-terminal domain (alpha-CTD) are required for full activation of rhaSR operon.  A direct or indirect interaction between CRP, RhaR and alpha-CTD has been suggested.
>110|P09377|L-rhamnose operon regulatory protein rhaS|Escherichia coli|AraC
The binding site for RhaS overlaps the -35 region of both the rhaBAD and the rhaT promoters by 4 bp.
Mutational studies directed to define interactions between RhaS and sigma 70 suggest that RhaS D241 and sigma-70 R599 are interacting residues in both promoters. In addition, molecular modelling suggests that sigma-70 R599 residue is located in very close proximity to RhaS D241. More than 50% of XylS/AraC family members have Asp or Glu at the position of RhaSD241, suggesting that this interaction with sigma-70 may be conserved.
CRP interaction with alpha-CTD may not be required for rhaBAD activation; however, alpha-CTD does contribute to full activation, probably through interactions with DNA and possibly RhaS.
>114|P16114|Regulatory protein rns|Escherichia coli|AraC
When Rns binds site II, which overlaps the -35 hexamer, it is probable that Rns makes direct contact with the sigma and alpha subunits of the RNA-polymerase.
>166|P07859|XylDLEGF operon transcriptional activator|Pseudomonas putida|AraC
XylS-dependent transcription from Pm is mediated by RNA polymerase with sigma 32 in the early exponential phase of growth upon addition of 3MB, which induces the heat shock response, and with sigma 38 in the late exponential phase or stationary phase.
A direct contact between XylS and the RNA-polymerase alpha subunit involving the 289-291 pocket of the alpha-CTD end has been identified.
>387|Q46985|Regulator of the 4HPA-hydroxylase operon|Escherichia coli|AraC
The -35 box of the Pbc promoter clearly deviates from the consensus sigma 70 promoters of E. coli. Upstream of this region two direct repeats can be found, a characteristic often observed in promoters regulated by the XylS/AraC family of proteins.
>393|Q51597|Cam repressor|Pseudomonas putida|TetR
The camR gene is transcribed by sigma-70 RNA polymerase.
Transcription from the camDCAB promoter by sigma-70 RNA polymerase was not observed.
It seems that CamR and RNA polymerase coexist on the promoter in a nonproductive complex.
>1368|O30507|Arginine regulatory protein (Transcriptional regulator ArgR) (ArgR regulatory protein)|Pseudomonas aeruginosa|AraC
In gdhB a sequence similar to the -10 region of the consensus of sigma-70 promoter of E. coli is located in the apropriate position, but a sequence resembling a -35 sequence is not evident.