RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: yhjA
Gene(s): ccp   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR and OxyR, which occupy the yhjAp promoter simultaneously, respond to two seemingly incompatible signals: oxygen starvation and peroxide stress Partridge JD,2007
Evidence: [COMP-AINF] Inferred computationally without human oversight
Reference(s): [1] Partridge JD., et al., 2007
Promoter
Name: yhjAp
+1: 3669261
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 73
Sequence: tcatgtaattgattgattcctatcaaaaagcgtatctccctgttttttatgatggctttgTctcgcagagacgtttgcagc
                           -35                       -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Partridge JD., et al., 2007
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator yhjAp 3669296 3669309 -41.5 atgtaattgaTTGATTCCTATCAAaaagcgtatc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
[OxyR,+] 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 OxyR activator yhjAp 3669317 3669333 -64.0 ctatcttattGATAGTTTATATTCATGtaattgattg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
proximal OxyR activator yhjAp 3669339 3669355 -86.0 tgatctgggtAATAGGCACAGGCTATCttattgatag nd [EXP-IEP-RNA-SEQ], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion


Reference(s)    

 [1] Partridge JD., Poole RK., Green J., 2007, The Escherichia coli yhjA gene, encoding a predicted cytochrome c peroxidase, is regulated by FNR and OxyR., Microbiology 153(Pt 5):1499-509

 [2] 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

 [3] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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