RegulonDB RegulonDB 10.8: Gene Form
   

yddE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yddE nhoA narV narW terminator TSS_1828 (cluster) TSS_1828 (cluster) yddEp5 yddEp5

Gene      
Name: yddE    Texpresso search in the literature
Synonym(s): ECK1458, EG11825, b1464
Genome position(nucleotides): 1534965 <-- 1535858 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.01
External database links:  
ASAP:
 ABE-0004886
ECHOBASE:
 EB1772
OU-MICROARRAY:
 b1464
PortEco:
 yddE
STRING:
 511145.b1464
COLOMBOS: yddE


Product      
Name: PF02567 family protein YddE
Synonym(s): YddE
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 32.319
Isoelectric point: 6.262
Motif(s):
 
Type Positions Sequence
8 -> 290 VDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFH

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016853 - isomerase activity
biological_process GO:0009058 - biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ECOCYC:
 EG11825-MONOMER
ECOLIWIKI:
 b1464
INTERPRO:
 IPR003719
MODBASE:
 P37757
PANTHER:
 PTHR13774
PDB:
 1QYA
PDB:
 1QY9
PDB:
 1SDJ
PFAM:
 PF02567
PRIDE:
 P37757
REFSEQ:
 NP_415981
SMR:
 P37757
UNIPROT:
 P37757


Operon      
Name: yddE         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Translational


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 yddEp5 1535869 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1828 (cluster) 1535879 reverse For this promoter, there
Read more > 		[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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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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