RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: dgoRKADT
Gene(s): dgoT, dgoD, dgoA, dgoK, dgoR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on a combination of genetic, functional, and biochemical analyses, regulatory elements were identified in the regulatory region of the dgoRKADT operon Belliveau NM,2018
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: dgoRp
+1: 3875185
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: tcatcacgctggtactacaaagttgccgcgttatgcatcgatcggggtaaagtagagaagAacatacagagcacaaggact
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
Reference(s): [1] Belliveau NM., et al., 2018
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator dgoRp 3875293 3875312 -117.0 attgttctttTTGTGATCTAAATTGTAGTAcaacaatata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
[DgoR,-] 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 DgoR repressor dgoRp 3875268 3875280 -88.5 acaatataagTTTGTACTACATTacacgcacgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [3], [4]
remote DgoR repressor dgoRp 3875290 3875301 -110.0 tgtgatctaaATTGTAGTACAAcaatataagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [3], [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.64 3871728 3871776 aattacagggCATGGTGAGCGGCTTCGCTATGCCCAAAATCTGGAGAAAGCTCGCTATggatattccc
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

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

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery


Reference(s)    

 [1] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [2] Arya G., Pal M., Sharma M., Singh B., Singh S., Agrawal V., Chaba R., 2021, Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli., Mol Microbiol 115(4):591-609

 [3] Lin Z., Sun Y., Liu Y., Tong S., Shang Z., Cai Y., Lin W., 2020, Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket., Front Microbiol 11:590330

 [4] Singh B., Arya G., Kundu N., Sangwan A., Nongthombam S., Chaba R., 2019, Molecular and Functional Insights into the Regulation of d-Galactonate Metabolism by the Transcriptional Regulator DgoR in Escherichia coli., J Bacteriol 201(4)

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