RegulonDB RegulonDB 11.0: Gene Form
   

dksA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gluQ sfsA dksA DksA DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp ppGpp ppGpp ppGpp TSS_285 TSS_285 TSS_284 (cluster) TSS_284 (cluster) TSS_283 TSS_283 TSS_282 TSS_282 TSS_281 (cluster) TSS_281 (cluster) TSS_280 TSS_280 TSS_279 TSS_279 TSS_278 TSS_278 TSS_277 (cluster) TSS_277 (cluster) dksAp3 dksAp3 dksAp1 dksAp1 dksAp2 dksAp2 TSS_275 (cluster) TSS_275 (cluster) TSS_274 TSS_274 gluQp1 gluQp1 pcnBp4 pcnBp4 pcnBp2 pcnBp2

Gene      
Name: dksA    Texpresso search in the literature
Synonym(s): ECK0144, EG10230, b0145, msmA
Genome position(nucleotides): 160149 <-- 160604
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.63
External database links:  
ASAP:
 ABE-0000499
CGSC:
 30521
ECHOBASE:
 EB0226
ECOLIHUB:
 dksA
OU-MICROARRAY:
 b0145
STRING:
 511145.b0145
COLOMBOS: dksA


Product      
Name: RNA polymerase-binding transcription factor DksA
Synonym(s): DksA, MsmA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.528
Isoelectric point: 4.774
Motif(s):
 
Type Positions Sequence Comment
4 -> 4 G UniProt: In Ref. 6; AA sequence..
71 -> 71 D UniProt: Does not increase ppGpp-dependent inhibition of transcription, but retains its ability to bind to RNAP; when associated with N-74. Increased transcription of its own RNA; when associated with N-74..
74 -> 74 D UniProt: Does not increase ppGpp-dependent inhibition of transcription, but retains its ability to bind to RNAP; when associated with N-71. Increased transcription of its own RNA; when associated with N-71..
94 -> 95 KL UniProt: In Ref. 1; AAA23687..
110 -> 143 DFGYCESCGVEIGIRRLEARPTADLCIDCKTLAE

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  5 - cell processes --> 5.5 - adaptations --> 5.5.3 - starvation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0097216 - guanosine tetraphosphate binding
biological_process GO:0010468 - regulation of gene expression
GO:0006302 - double-strand break repair
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Brown L., et al., 2002
External database links:  
ALPHAFOLD:
 P0ABS1
DIP:
 DIP-31875N
DISPROT:
 DP00414
ECOCYC:
 EG10230-MONOMER
ECOLIWIKI:
 b0145
INTERPRO:
 IPR012784
INTERPRO:
 IPR037187
INTERPRO:
 IPR000962
INTERPRO:
 IPR020460
INTERPRO:
 IPR020458
MINT:
 P0ABS1
PDB:
 7KHE
PDB:
 5W1T
PDB:
 5VSW
PDB:
 1TJL
PDB:
 7KHI
PFAM:
 PF01258
PRIDE:
 P0ABS1
PRINTS:
 PR00618
PRODB:
 PRO_000022453
PROSITE:
 PS01102
PROSITE:
 PS51128
REFSEQ:
 NP_414687
SMR:
 P0ABS1
UNIPROT:
 P0ABS1


Operon      
Name: sfsA-dksA-gluQ         
Operon arrangement:
Transcription unit        Promoter
dksA-yadB
dksA-yadB
dksA-gluQ
sfsA-dksA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


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 gluQp1 160143 reverse nd [ICWHO] [2]
  promoter TSS_274 160641 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_275 (cluster) 160652 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_277 (cluster) 160761 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_278 160873 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_279 160884 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_280 161071 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_281 (cluster) 161079 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_282 161142 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_283 161187 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_284 (cluster) 161195 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_285 161199 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Brown L., Gentry D., Elliott T., Cashel M., 2002, DksA affects ppGpp induction of RpoS at a translational level., J Bacteriol 184(16):4455-65

 [2] 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

 [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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