RegulonDB RegulonDB 10.8: Gene Form
   

nrdR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ribD yajI nrdR TSS_530 (cluster) TSS_530 (cluster) ribEp ribEp TSS_528 TSS_528 yajIp6 yajIp6 nrdRp nrdRp TSS_526 TSS_526

Gene      
Name: nrdR    Texpresso search in the literature
Synonym(s): ECK0407, EG11320, b0413, ybaD
Genome position(nucleotides): 433002 --> 433451 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.33
External database links:  
ASAP:
ABE-0001437
ECHOBASE:
EB1296
OU-MICROARRAY:
b0413
PortEco:
nrdR
STRING:
511145.b0413
COLOMBOS: nrdR


Product      
Name: NrdR transcriptional repressor
Synonym(s): NrdR, YbaD
Sequence: Get amino acid sequence Fasta Format
Regulator Family: NrdR
Cellular location: cytosol
Molecular weight: 17.229
Isoelectric point: 7.936
Motif(s):
 
Type Positions Sequence
49 -> 139 PRVVKSNDVREPFNEEKLRSGMLRALEKRPVSSDDVEMAINHIKSQLRATGEREVPSKMIGNLVMEQLKKLDKVAYIRFASVYRSFEDIKE
50 -> 136 RVVKSNDVREPFNEEKLRSGMLRALEKRPVSSDDVEMAINHIKSQLRATGEREVPSKMIGNLVMEQLKKLDKVAYIRFASVYRSFED
3 -> 34 CPFCFAVDTKVIDSRLVGEGSSVRRRRQCLVC

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0003690 - double-stranded DNA binding
GO:0008270 - zinc ion binding
biological_process GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-31842N
ECOCYC:
EG11320-MONOMER
ECOLIWIKI:
b0413
INTERPRO:
IPR005144
INTERPRO:
IPR003796
MINT:
MINT-1276184
PANTHER:
PTHR30455
PFAM:
PF03477
PRIDE:
P0A8D0
PRODB:
PRO_000023410
PROSITE:
PS51161
REFSEQ:
NP_414947
UNIPROT:
P0A8D0


Operon      
Name: nrdR-ribDE-nusB-thiL-pgpA         
Operon arrangement:
Transcription unit        Promoter
nrdR-ribDE-nusB-thiL-pgpA
ribE-nusB-thiL-pgpA


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_526 432975 forward nd [RS-EPT-CBR] [1]
  promoter yajIp6 433034 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_528 434501 forward nd [RS-EPT-CBR] [1]
  promoter TSS_530 (cluster) 434511 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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


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