RegulonDB RegulonDB 11.1: Operon Form
   

tomB-hha operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: tomB-hha
Gene(s): hha, tomB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: tomBp
+1: 480794
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: attgtaatttttcgtaataatgcgatgaaaacctgcaaagagtggcttatagttaagctaAcaaacgagagggcaagtcca
                              -35                    -10    +1                   
Note(s): The tomBp1 promoter is significantly affected by ectopic production of a nanoRNase during stationary-phase growth Vvedenskaya IO,2012
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Yamamoto K., et al., 2006
TF binding sites (TFBSs)
[BasR,+] 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 BasR-phosphorylated activator tomBp 481179 481198 -394.5 ataacctacgAACATTAAGGAGTAATTGAAccaccaactc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
[CpxR,+] 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 CpxR-phosphorylated activator tomBp 480843 480844 -50.0 attgtaatttTtcgtaataat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
[PdhR,-] 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 PdhR repressor tomBp 480964 480980 -178.0 gcaatcctggTATTAGTGTCACCAATTtcatctggcg nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

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

 [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] Yamamoto K., Ishihama A., 2006, Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli., Biosci Biotechnol Biochem 70(7):1688-95

 [3] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92

 [4] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

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