RegulonDB RegulonDB 10.8: Gene Form
   

pdeF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdeF ppx yfgG FNR yfgGp yfgGp yfgGp5 yfgGp5 yfgGp6 yfgGp6 yfgGp7 yfgGp7 yfgFp yfgFp

Gene      
Name: pdeF    Texpresso search in the literature
Synonym(s): ECK2499, G7314, b2503, yfgF
Genome position(nucleotides): 2626695 <-- 2628938 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.61
External database links:  
ASAP:
ABE-0008240
ECHOBASE:
EB3954
OU-MICROARRAY:
b2503
PortEco:
yfgF
STRING:
511145.b2503
COLOMBOS: pdeF


Product      
Name: cyclic di-GMP phosphodiesterase PdeF
Synonym(s): PdeF, YfgF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 85.608
Isoelectric point: 8.916
Motif(s):
 
Type Positions Sequence
43 -> 65 VFLFYLPLALMISMMMFFSWAAL
80 -> 102 LGFYETLSLTANFIIIIILCWGG
129 -> 151 IVFPATLFLILFQFAAFVGLLAS
240 -> 259 IFSTNYTLSLLLPLMMWGAM
493 -> 744 KVAMMNRLQQALEHNHFFLMAQPITGMRGDVYHEILLRMKGENDELISPDSFLPVAHEFGLSSSIDMWVIEHTLQFMAENRAKMPAHRFAINLSPTSVCQARFPVEVSQLLAKYQIEAWQLIFEVTESNALTNVKQAQITLQHLQELGCQIAIDDFGTGYASYARLKNVNADLLKIDGSFIRNIVSNSLDYQIVASICHLARMKKMLVVAEYVENEEIREAVLSLGIDYMQGYLIGKPQPLIDTLNEIEPIR

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0016787 - hydrolase activity
GO:0000166 - nucleotide binding
GO:0042803 - protein homodimerization activity
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity
biological_process GO:0070301 - cellular response to hydrogen peroxide
GO:0071454 - cellular response to anoxia
GO:1900190 - regulation of single-species biofilm formation
External database links:  
DIP:
DIP-12038N
ECOCYC:
G7314-MONOMER
ECOLIWIKI:
b2503
INTERPRO:
IPR007895
INTERPRO:
IPR035919
INTERPRO:
IPR001633
INTERPRO:
IPR000160
PFAM:
PF00563
PFAM:
PF05231
PRIDE:
P77172
PROSITE:
PS50883
REFSEQ:
NP_416998
SMART:
SM00052
SMART:
SM00267
SMR:
P77172
UNIPROT:
P77172


Operon      
Name: pdeF         
Operon arrangement:
Transcription unit        Promoter
yfgF


Transcriptional Regulation      
Display Regulation             
Activated by: FNR


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 yfgGp7 2629085 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter yfgGp6 2629186 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter yfgGp5 2629252 forward Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [1], [2]


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] 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

 [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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