RegulonDB RegulonDB 10.10: Gene Form
   

yrdB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rrsD aroE tsaC yrdA yrdB Fis Fis Fis Fis Fis DksA DksA-ppGpp DksA-ppGpp ppGpp yrdBp4 yrdBp4 yrdBp1 yrdBp1 TSS_3601 TSS_3601 rrsDp1 rrsDp1 rrsDp2 rrsDp2 TSS_3600 TSS_3600

Gene      
Name: yrdB    Texpresso search in the literature
Synonym(s): ECK3267, G7697, b3280
Genome position(nucleotides): 3429766 <-- 3430023 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.22
External database links:  
ASAP:
 ABE-0010761
ECHOBASE:
 EB2688
ECOLIHUB:
 yrdB
OU-MICROARRAY:
 b3280
STRING:
 511145.b3280
COLOMBOS: yrdB


Product      
Name: DUF1488 domain-containing protein YrdB
Synonym(s): YrdB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 10.007
Isoelectric point: 3.91
Motif(s):
 
Type Positions Sequence
5 -> 84 IQFPDREEWDENKKCVCFPALVNGMQLTCAISGESLAYRFTGDTPEQWLASFRQHRWDLEEEAENLIQEQSEDDQGWVWL

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
 G7697-MONOMER
ECOLIWIKI:
 b3280
INTERPRO:
 IPR036692
INTERPRO:
 IPR009962
PFAM:
 PF07369
PRIDE:
 P45795
REFSEQ:
 NP_417739
SMR:
 P45795
UNIPROT:
 P45795


Operon      
Name: yrdD-tsaC-aroE-yrdB         
Operon arrangement:
Transcription unit        Promoter
yrdD-rimN-aroE-yrdB


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_3600 3428877 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3601 3429211 forward nd [RS-EPT-CBR] [1]
  promoter yrdBp1 3430062 reverse nd [ICWHO] [2]
  promoter yrdBp4 3430088 reverse nd [ICWHO] [2]


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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