RegulonDB RegulonDB 11.1: Operon Form
   

waaH operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: yibD
Gene(s): waaH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yibDp1
+1: 3790149
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 68
Sequence: ctgctctcattatctctctaccctgaagtgactctctcacctgtaaaaataatatctcacAggcttaatagtttcttaata
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[NsrR,-] 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
remote NsrR repressor yibDp1 3790259 3790270 -115.0 ataatctgttAAATATGTAAAAtcctgtcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
[PhoB,+] 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 PhoB-phosphorylated activator yibDp1 3790199 3790219 -59.5 tgtgctgatcTCTTATATAGCTGCTCTCATTatctctctac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
remote PhoB-phosphorylated activator yibDp1 3790249 3790276 -113.0 ctgaggataaTCTGTTAAATATGTAAAATCCTGTCAGTgtaataaaga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]


Transcription unit       
Name: yibD
Gene(s): waaH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.4 3790287 3790310 acacgaacaaGGGCTGGTATTCCAGCCCTTTTAtctgaggata
  anti-terminator -8.74 3790306 3790351 cgttcgggccAGTCCGGGAAAGTTATTCTGAGCTGGGATTAACACGAACAAGGGCtggtattcca
  anti-anti-terminator -8.5 3790337 3790382 cgatgatttcCAGAAGGGCTTTGACGCTATGCGTTCGGGCCAGTCCGGGAAAGTTattctgagct
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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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


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] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [3] Baek JH., Lee SY., 2006, Novel gene members in the Pho regulon of Escherichia coli., FEMS Microbiol Lett 264(1):104-9

RegulonDB