RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ybdN
Gene(s): ybdN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ybdNp
+1: 636686
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 117
Sequence: atttattgaccgtctaaatgagagtttttgatatataactacagacagctactataacttTcatctatttattcacagcgc
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[ArcA,+] 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 ArcA-phosphorylated activator ybdNp 636615 636629 64.5 acagtgtttaCTTTATAATTAACAGacttatctca nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
[CysB,+] 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 CysB-O-acetyl-L-serine activator ybdNp 636843 636885 -177.5 gatttactggGAATAGTCCCCTATGAACTTTATAATTCCTACCGTGACTTTCTtaacttaaaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [3]
[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 ybdNp 636706 636719 -26.5 atgagagtttTTGATATATAACTAcagacagcta nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
remote FNR activator ybdNp 636983 636996 -303.5 tcagcaggggTTGATGATATTCAAatggaaatag nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]


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


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., Scott C., Tang Y., Poole RK., Green J., 2006, Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions., J Biol Chem 281(38):27806-15

 [3] Kawano Y., Ohtsu I., Takumi K., Tamakoshi A., Nonaka G., Funahashi E., Ihara M., Takagi H., 2015, Enhancement of L-cysteine production by disruption of yciW in Escherichia coli., J Biosci Bioeng 119(2):176-9

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