RegulonDB RegulonDB 10.8: Gene Form
   

dgoR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dgoK dgoR yidX dgoA dgoD CRP DgoR DgoR TSS_4257 TSS_4257 dgoRp dgoRp

Gene      
Name: dgoR    Texpresso search in the literature
Synonym(s): ECK3687, G7789, b3694, b3695, b4479, yidW
Genome position(nucleotides): 3874471 <-- 3875160 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.36
External database links:  
ASAP:
 ABE-0174108
ECHOBASE:
 EB1669
OU-MICROARRAY:
 b3694
PortEco:
 dgoR
STRING:
 511145.b4479
COLOMBOS: dgoR


Product      
Name: DNA-binding transcriptional regulator DgoR
Synonym(s): DgoR, YidW
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 26.08
Isoelectric point: 5.397
Motif(s):
 
Type Positions Sequence
1 -> 71 MTLNKTDRIVITLGKQIVHGKYVPGSPLPAEAELCEEFATSRNIIREVFRSLMAKRLIEMKRYRGAFVAPR
111 -> 112 RW
99 -> 218 SEVRNLVEPAIARWAAERATSSDLAQIESALNEMIANNQDREAFNEADIRYHEAVLQSVHNPVLQQLSIAISSLQRAVFERTWMGDEANMPQTLQEHKALFDAIRHQDGDAAEQAALTMI
31 -> 50 EAELCEEFATSRNIIREVFR
7 -> 68 DRIVITLGKQIVHGKYVPGSPLPAEAELCEEFATSRNIIREVFRSLMAKRLIEMKRYRGAFV

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0098531 - ligand-activated transcription factor activity
GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0042802 - identical protein binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
GO:0001017 - bacterial-type RNA polymerase regulatory region DNA binding
GO:0001217 - DNA-binding transcription repressor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:2000143 - negative regulation of DNA-templated transcription, initiation
GO:0010677 - negative regulation of cellular carbohydrate metabolic process
Note(s): Note(s): ...[more].
Evidence: [APPINH] Assay of protein partially-purified from its native host
[HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay
[IEP] Inferred from expression pattern
[IPI] Inferred from physical interaction
Reference(s): [1] Belliveau NM., et al., 2018
[2] Perez-Rueda E., et al., 2004
[3] Rigali S., et al., 2002
[4] Singh B., et al., 2019
External database links:  
DIP:
 DIP-9435N
ECOCYC:
 G7790-MONOMER
ECOLIWIKI:
 b4479
INTERPRO:
 IPR011711
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR008920
INTERPRO:
 IPR000524
MODBASE:
 P31460
PFAM:
 PF00392
PFAM:
 PF07729
PRIDE:
 P31460
PRINTS:
 PR00035
PROSITE:
 PS50949
REFSEQ:
 YP_026239
SMART:
 SM00345
SMART:
 SM00895
SMR:
 P31460
UNIPROT:
 P31460


Operon      
Name: dgoRKADT         
Operon arrangement:
Transcription unit        Promoter
dgoRKADT


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: DgoR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4257 3875186 reverse nd [RS-EPT-CBR] [5]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


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] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] Rigali S., Derouaux A., Giannotta F., Dusart J., 2002, Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies., J Biol Chem 277(15):12507-15

 [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)

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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