RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: yhdWXYZ
Gene(s): yhdW, yhdX, yhdY, yhdZ   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Zimmer DP., et al., 2000
Promoter
Name: yhdWp
+1: 3418972
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 70
Sequence: cagcttattgcgacgcgaaatcgtgcgcaaaagctggcactacttttgcttataagaggaTggccacagacaggtaaaaga
Note(s): 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-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
Reference(s): [2] Reitzer L., et al., 2001
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
remote NtrC-phosphorylated activator yhdWp 3418838 3418854 -126.0 gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]
remote NtrC-phosphorylated activator yhdWp 3418868 3418884 -96.0 gtttcattttCGCACCATTGCGGGGCGctgtttttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]


Evidence    

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] 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

 [2] 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

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