RegulonDB RegulonDB 11.1: 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] 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: ddpXp1
+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: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [3] Huerta AM., et al., 2003
[4] Reitzer L., et al., 2001
[5] Zhao K., et al., 2010
TF binding sites (TFBSs)
[NtrC,+] 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 NtrC-phosphorylated activator ddpXp1 1563187 1563203 -88.0 tgcactacgcTGCACAAATGTTGATCAaaagttaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
remote NtrC-phosphorylated activator ddpXp1 1563208 1563224 -109.0 cttcccctctTGCACCAAAACTGCACTacgctgcaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


Transcription unit       
Name: ddpXABCDF
Gene(s): ddpF, ddpD, ddpC, ddpB, ddpA, ddpX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] 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                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
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: [IC-ADJ-GENES-SAME-BIO-PROCESS] 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                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Lessard IA., et al., 1998


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

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP] Inferred from expression pattern

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Lessard IA., Pratt SD., McCafferty DG., Bussiere DE., Hutchins C., Wanner BL., Katz L., Walsh CT., 1998, Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function., Chem Biol 5(9):489-504

 [2] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

 [3] 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

 [4] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [5] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

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