RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: ydhYVWXUT
Gene(s): ydhT, ydhU, ydhX, ydhW, ydhV, ydhY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Partridge JD., et al., 2008
Promoter
Name: ydhYp
+1: 1754642
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 165
Sequence: tgtaattttaattgataacgatcaatgttaagggctcagaataatcacattattttttctCctaaccataaaggattagtt
                            -35               -10           +1                   
Evidence: [TIM]
Reference(s): [1] Partridge JD., et al., 2008
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator ydhYp 1754678 1754691 -42.5 gtaattttaaTTGATAACGATCAAtgttaagggc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1], [2]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor ydhYp 1754620 1754635 15.0 tctcctaaccATAAAGGATTAGTTTAtcggcgttaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
proximal NarL-Phosphorylated repressor ydhYp 1754629 1754644 6.0 attattttttCTCCTAACCATAAAGGattagtttat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
proximal NarL-Phosphorylated repressor ydhYp 1754650 1754665 -16.0 ttaagggctcAGAATAATCACATTATtttttctcct nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
proximal NarL-Phosphorylated4 repressor ydhYp 1754676 1754691 -42.0 gtaattttaaTTGATAACGATCAATGttaagggctc nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1]
[NarP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-Phosphorylated repressor ydhYp 1754625 1754632 15.0 cctaaccataAAGGATTAgtttatcggc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
proximal NarP-Phosphorylated repressor ydhYp 1754634 1754641 6.0 attttttctcCTAACCATaaaggattag nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
Note(s): 4Although this site (-42 heptamer) had significant contribution in in vivo assays, no clear protection by NarL was detected in DNase footprint analyses. However, this suggests that there are other factors in vivo that lead to occupation of the -42 heptamer by NarL in the presence of nitrate Partridge JD,2008.2Although this site (-42 heptamer) had significant contribution in in vivo assays, no clear protection by NarL was detected in DNase footprint analyses. However, this suggests that there are other factors in vivo that lead to occupation of the -42 heptamer by NarL in the presence of nitrate Partridge JD,2008.


Transcription unit       
Gene(s): ydhT, ydhU, ydhX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


Transcription unit       
Gene(s): ydhW, ydhV, ydhY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown repressor       [IMP] [1]
[3]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Partridge JD., Browning DF., Xu M., Newnham LJ., Scott C., Roberts RE., Poole RK., Green J., 2008, Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP., Microbiology 154(Pt 2):608-18

 [2] Kang Y., Weber KD., Qiu Y., Kiley PJ., Blattner FR., 2005, Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function., J Bacteriol 187(3):1135-60

 [3] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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