RegulonDB RegulonDB 10.7: Operon Form
   

ydcSTUV-patD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ydcSTUV-patD
Gene(s): ydcS, ydcT, ydcU, ydcV, patD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the ydcSTUV-patD operon is induced under nitrogen-limited growth |CITS:[ 23531166]|. It also was demonstrated by in vitro transcription analysis and gene expression analysis that this operon is activated by the protein Nac and by σ38. Two putative -10 boxes for σ38 and two DNA-binding sites similar to the consensus recognized by Nac were found, but it has not been demonstrated which of these sequences are functional; therefore, we linked to the operon only the -10 box, which is more conserved relative to the consensus σ38 and the DNA-binding site that is located closer to this promoter |CITS:[ 23531166]|.
Evidence: [ITC] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 2013
[2] Zimmer DP., et al., 2000
Promoter
Name: ydcSp1
+1: 1511599
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 55
Sequence: gaataaattttctcaggggcgaaggtgtgcctgcaagccgccgtctatggttaaacaaggAgatatttttacggcacggcg
                                            -10             +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation of which the majority of the promoters, whose transcription start site was determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
Reference(s): [1] Schneider BL., et al., 2013
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac activator ydcSp1 1511541 1511555 -51.0 cacaacctgaATAAATTTTCTCAGGggcgaaggtg nd [APIORCISFBSCS], [GEA], [IDA] [1]


Transcription unit       
Name: ydcSTUV-patD
Gene(s): ydcS, ydcT, ydcU, ydcV, patD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 2013
[2] Zimmer DP., et al., 2000


Transcription unit       
Name: ydcSTUV-patD
Gene(s): ydcS, ydcT, ydcU, ydcV, patD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 2013
[2] Zimmer DP., et al., 2000


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





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