RegulonDB RegulonDB 10.9: Gene Form
   

yrdA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rrsD aroE 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: yrdA    Texpresso search in the literature
Synonym(s): ECK3266, G7696, b3279
Genome position(nucleotides): 3429236 --> 3429790 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.83
External database links:  
ASAP:
ABE-0010759
ECHOBASE:
EB2687
ECOLIHUB:
yrdA
OU-MICROARRAY:
b3279
STRING:
511145.b3279
COLOMBOS: yrdA


Product      
Name: hexapeptide repeats-containing protein YrdA
Synonym(s): YrdA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.245
Isoelectric point: 5.207
Motif(s):
 
Type Positions Sequence
13 -> 47 PQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRG
97 -> 130 GCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLV

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032991 - protein-containing complex
molecular_function GO:0008270 - zinc ion binding
GO:0042802 - identical protein binding
External database links:  
DIP:
DIP-48232N
ECOCYC:
G7696-MONOMER
ECOLIWIKI:
b3279
INTERPRO:
IPR011004
INTERPRO:
IPR001451
MODBASE:
P0A9W9
PDB:
3TIS
PDB:
3TIO
PFAM:
PF00132
PRIDE:
P0A9W9
REFSEQ:
NP_417738
SMR:
P0A9W9
SWISSMODEL:
P0A9W9
UNIPROT:
P0A9W9


Operon      
Name: yrdA         
Operon arrangement:
Transcription unit        Promoter
yrdA


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 Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yrdBp4 3430088 reverse Similarity to the consensus
Read more >
[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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