RegulonDB RegulonDB 11.1: Operon Form
   

ppdD-hofBC operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ppdD-hofBC
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ppdD-hofBC
Gene(s): hofC, hofB, ppdD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ppdDp
+1: 117705
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 156
Sequence: tgcgttttcgctaatagttgacagatttatccgctccatcgcgggcggataatctcccctTccccaactttcttcgtaacg
                               -35                     -10  +1                   
Note(s): ppdDp belongs to the group of promoters under control of CRP and Sxy, called CRP-S (Sxy-dependent CRP sites) Cameron AD,2006
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator ppdDp 117675 117696 20.5 ttccccaactTTCTTCGTAACGCCTCGCAAATttcttgtctt nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.9 117572 117594 cctgtgctgaTGGCGTTTGCCAAAGTAGCGCCaaccaaatca
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [2] Cameron AD., Redfield RJ., 2006, Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria., Nucleic Acids Res 34(20):6001-14

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