RegulonDB RegulonDB 10.9: Gene Form
   

dcuB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fumB dcuB dcuR dcuS DcuR DcuR NarL CRP FNR NarL NarL NarL NarL NarL FNR FNR FNR dcuBp2 dcuBp2 TSS_4925 TSS_4925 TSS_4924 TSS_4924 dcuBp dcuBp TSS_4923 (cluster) TSS_4923 (cluster) fumBp fumBp

Gene      
Name: dcuB    Texpresso search in the literature
Synonym(s): ECK4116, EG10006, b4123, genF
Genome position(nucleotides): 4347404 <-- 4348744 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.27
External database links:  
ASAP:
 ABE-0013503
CGSC:
 34479
ECHOBASE:
 EB0006
ECOLIHUB:
 dcuB
OU-MICROARRAY:
 b4123
STRING:
 511145.b4123
COLOMBOS: dcuB


Product      
Name: anaerobic C4-dicarboxylate transporter DcuB
Synonym(s): DcuB, GenF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 47.935
Isoelectric point: 7.878
Motif(s):
 
Type Positions Sequence
6 -> 376 QLIIILICLFYGARKGGIALGLLGGIGLVILVFVFHLQPGKPPVDVMLVIIAVVAASATLQASGGLDVMLQIAEKLLRRNPKYVSIVAPFVTCTLTILCGTGHVVYTILPIIYDVAIKNNIRPERPMAASSIGAQMGIIASPVSVAVVSLVAMLGNVTFDGRHLEFLDLLAITIPSTLIGILAIGIFSWFRGKDLDKDEEFQKFISVPENREYVYGDTATLLDKKLPKSNWLAMWIFLGAIAVVALLGADSDLRPSFGGKPLSMVLVIQMFMLLTGALIIILTKTNPASISKNEVFRSGMIAIVAVYGIAWMAETMFGAHMSEIQGVLGEMVKEYPWAYAIVLLLVSKFVNSQAAALAAIVPVALAIGVDP
21 -> 39 GGIALGLLGGIGLVILVFV
56 -> 73 IAVVAASATLQASGGLDV
367 -> 384 PVALAIGVDPAYIVASAP
119 -> 119 D

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0015556 - C4-dicarboxylate transmembrane transporter activity
GO:0005469 - succinate:fumarate antiporter activity
biological_process GO:0009061 - anaerobic respiration
GO:0015740 - C4-dicarboxylate transport
GO:0015741 - fumarate transport
GO:0071422 - succinate transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Engel P., et al., 1992
[2] Scheu PD., et al., 2010
External database links:  
ECOCYC:
 DCUB-MONOMER
ECOLIWIKI:
 b4123
INTERPRO:
 IPR004668
PANTHER:
 PTHR36106
PFAM:
 PF03605
PRIDE:
 P0ABN9
PRODB:
 PRO_000022413
REFSEQ:
 NP_418547
UNIPROT:
 P0ABN9


Operon      
Name: dcuB-fumB         
Operon arrangement:
Transcription unit        Promoter
fumB
dcuB-fumB
dcuB-fumB


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, FNR, DcuR
Repressed by: NarL
Growth Conditions:

[1] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glucose 0.4%| 37.0 C
E: Escherichia coli| crp knockout mutant| M9 minimal medium| fumarate 50 mM; glucose 0.4%| 37.0 C

[2] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%; nitrate| 37.0 C

[3] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; fumarate 50 mM; glycerol 0.4%| 37.0 C

[4] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| fnr knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[5] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[6] 

C: Escherichia coli| narL knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| narL knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%; nitrate| 37.0 C

[7] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%; malate 50 mM| 37.0 C

[8] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%; succinate 50 mM| 37.0 C

[9] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; glycerol 0.4%| oxygen atom| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; glycerol 0.4%| 37.0 C

[10] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| fumarate 50 mM; glucose 0.4%| 37.0 C

[11] 

C: Escherichia coli| L broth| fumarate 50 mM; glycerol 0.4%| oxygen atom| mid exponential phase
E: Escherichia coli| L broth| fumarate 50 mM; glycerol 0.4%| mid exponential phase

[12] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[13] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| casamino acids 0.05%; glycerol 0.4%; nitrate 50 mM| 37.0 C

[14] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.5%; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C

[15] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; glucose 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glucose 0.4%| 37.0 C

[16] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; aspartate 50 mM; glycerol 0.4%| 37.0 C

[17] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| oxygen atom| 37.0 C
E: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[18] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glucose 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[19] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| crp knockout mutant| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C

[20] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| oxygen atom| 37.0 C
E: Escherichia coli| arcA knockout mutant| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| oxygen atom| 37.0 C

[21] 

C: Escherichia coli| fnr knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| oxygen atom| 37.0 C
E: Escherichia coli| fnr knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[22] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; glycerol 0.4%| 37.0 C

[23] 

C: Escherichia coli| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| arcA knockout mutant| M9 minimal medium| fumarate 50 mM; glycerol 0.4%| 37.0 C

[24] 

C:
E: Escherichia coli| L broth| fumarate 50 mM; glycerol 0.4%

[25] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| M9 minimal medium| TMAO 50 mM; glycerol 0.4%; maleate 50 mM| 37.0 C

[26] 

C: Escherichia coli| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C
E: Escherichia coli| narL knockout mutant| M9 minimal medium| TMAO 50 mM; casamino acids 0.05%; fumarate 50 mM; glycerol 0.4%| 37.0 C

[27] 

C: Escherichia coli| M9 minimal medium| casamino acids 0.05%; glycerol 0.4%; nitrate 50 mM| oxygen atom| 37.0 C
E: Escherichia coli| M9 minimal medium| casamino acids 0.05%; glycerol 0.4%; nitrate 50 mM| 37.0 C


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_4923 (cluster) 4347981 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_4924 4348786 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4925 4348841 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Engel P., Kramer R., Unden G., 1992, Anaerobic fumarate transport in Escherichia coli by an fnr-dependent dicarboxylate uptake system which is different from the aerobic dicarboxylate uptake system., J Bacteriol 174(17):5533-9

 [2] Scheu PD., Kim OB., Griesinger C., Unden G., 2010, Sensing by the membrane-bound sensor kinase DcuS: exogenous versus endogenous sensing of C(4)-dicarboxylates in bacteria., Future Microbiol 5(9):1383-402

 [3] 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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