RegulonDB RegulonDB 10.8: Gene Form
   

ydfD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intQ ydfE insD7 ydfD dicB ynfP dicF terminator anti-terminator anti-anti-terminator TSS_1869 TSS_1869 dicBp dicBp

Gene      
Name: ydfD    Texpresso search in the literature
Synonym(s): ECK1570, EG11303, b1576
Genome position(nucleotides): 1649794 --> 1649985 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 43.23
External database links:  
ASAP:
 ABE-0005262
ECHOBASE:
 EB1280
OU-MICROARRAY:
 b1576
PortEco:
 ydfD
STRING:
 511145.b1576
COLOMBOS: ydfD


Product      
Name: Qin prophage; lysis protein
Synonym(s): YdfD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 6.842
Isoelectric point: 4.444
Motif(s):
 
Type Positions Sequence
4 -> 61 AFVLVLTVFLVSGEPVDIAVSVHRTMQECMTAATEQKIPGNCYPVDKVIHQDNIEIPA

 
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
biological_process GO:0044659 - viral release from host cell by cytolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ECOCYC:
 EG11303-MONOMER
ECOLIWIKI:
 b1576
INTERPRO:
 IPR009954
PFAM:
 PF07358
PRIDE:
 P29010
REFSEQ:
 NP_416093
UNIPROT:
 P29010


Operon      
Name: dicB-ydfDE-insD7-intQ         
Operon arrangement:
Transcription unit        Promoter
dicB-ydfDE-insD-intQ


Transcriptional Regulation      
Display Regulation             
Repressed by: DicA


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_1869 1651862 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [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] 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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