RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit          
Name: ddpXABCDF
Gene(s): ddpF, ddpD, ddpC, ddpB, ddpA, ddpX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lessard IA., et al., 1998
[2] Zimmer DP., et al., 2000
Promoter
Name: ddpXp
+1: 1563107
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 31
Sequence: ttaagccagcattctggcgcttatcccggcatggcatgagatctgcataagcggaaagcgCagcaatttttgtcttataca
                                -24         -12             +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [AIPP]
[HIPP]
[IEP]
Reference(s): [3] Reitzer L., et al., 2001
[4] Zhao K., et al., 2010
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 NtrC-Pasp activator ddpXp 1563187 1563203 -88.0 tgcactacgcTGCACAAATGTTGATCAaaagttaaaa nd [AIBSCS], [GEA] [2]
remote NtrC-Pasp activator ddpXp 1563208 1563224 -109.0 cttcccctctTGCACCAAAACTGCACTacgctgcaca nd [AIBSCS], [GEA] [2]


Transcription unit       
Name: ddpXABCDF
Gene(s): ddpF, ddpD, ddpC, ddpB, ddpA, ddpX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lessard IA., et al., 1998
Promoter
Name: ddpXp2
+1: 1563201
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 125
Sequence: tacgattccgggagattccttccttaacttcccctcttgcaccaaaactgcactacgctgCacaaatgttgatcaaaagtt
                                                -10         +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
Reference(s): [1] Lessard IA., et al., 1998


Transcription unit       
Name: ddpXABCDF
Gene(s): ddpF, ddpD, ddpC, ddpB, ddpA, ddpX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lessard IA., et al., 1998
Promoter
Name: ddpXp3
+1: 1563249
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 173
Sequence: gggttttcatttaacgtgacactgtcacttaaatactgtgatttcagctacgattccgggAgattccttccttaacttccc
                                                -10         +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
Reference(s): [1] Lessard IA., et al., 1998





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