RegulonDB RegulonDB 11.1: Gene Form
   

pdeB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdeB ylaC ybaA TSS_612 TSS_612 TSS_611 TSS_611

Gene      
Name: pdeB    Texpresso search in the literature
Synonym(s): ECK0451, G6252, b0457, ylaB
Genome position(nucleotides): 477067 <-- 478617
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.03
External database links:  
ASAP:
 ABE-0001584
ECHOBASE:
 EB3988
ECOLIHUB:
 ylaB
OU-MICROARRAY:
 b0457
STRING:
 511145.b0457
COLOMBOS: pdeB


Product      
Name: c-di-GMP phosphodiesterase PdeB
Synonym(s): PdeB, YlaB
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol,periplasmic space
Molecular weight: 58.72
Isoelectric point: 6.084
Motif(s):
 
Type Positions Sequence Comment
6 -> 26 LVGLISGVLILSVLLPVGLSI UniProt: Helical.
39 -> 242 EELDTYSSRVAIRANKVATQGKDALQELERWQGAACSEAHLMEMRRVSYSYRYIQEVAYIDNNVPQCSSLEHESPPDTFPEPGKISKDGYRVWLTSHNDLGIIRYMVAMGTAHYVVMIDPASFIDVIPYSSWQIDAAIIGNAHNVVITSSDEIAQGIITRLQKTPGEHIENNGIIYDILPLPEMNISIITWASTKMLQKGWHRQ
242 -> 262 QVFIWLPLGLVIGLLAAMFVL UniProt: Helical.
268 -> 516 IQSPHHRLQDAIENRDICVHYQPIVSLANGKIVGAEALARWPQTDGSWLSPDSFIPLAQQTGLSEPLTLLIIRSVFEDMGDWLRQHPQQHISINLESPVLTSEKIPQLLRDMINHYQVNPRQIALELTEREFADPKTSAPIISRYREAGHEIYLDDFGTGYSSLSYLQDLDVDILKIDKSFVDALEYKNVTPHIIEMAKTLKLKMVAEGIETSKQEEWLRQHGVHYGQGWLYSKALPKEDFLRWAEQHL UniProt: EAL.
274 -> 501 RLQDAIENRDICVHYQPIVSLANGKIVGAEALARWPQTDGSWLSPDSFIPLAQQTGLSEPLTLLIIRSVFEDMGDWLRQHPQQHISINLESPVLTSEKIPQLLRDMINHYQVNPRQIALELTEREFADPKTSAPIISRYREAGHEIYLDDFGTGYSSLSYLQDLDVDILKIDKSFVDALEYKNVTPHIIEMAKTLKLKMVAEGIETSKQEEWLRQHGVHYGQGWLYSK

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0016787 - hydrolase activity
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity
Note(s): Note(s): ...[more].
Reference(s): [1] Sarenko O., et al., 2017
External database links:  
ALPHAFOLD:
 P77473
ECOCYC:
 G6252-MONOMER
ECOLIWIKI:
 b0457
INTERPRO:
 IPR024744
INTERPRO:
 IPR001633
INTERPRO:
 IPR035919
PFAM:
 PF00563
PFAM:
 PF12792
PRIDE:
 P77473
PROSITE:
 PS50883
REFSEQ:
 NP_414990
SMART:
 SM00052
SMR:
 P77473
UNIPROT:
 P77473


Operon      
Name: pdeB         
Operon arrangement:
Transcription unit        Promoter
pdeB


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_611 478612 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_612 478642 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] Sarenko O., Klauck G., Wilke FM., Pfiffer V., Richter AM., Herbst S., Kaever V., Hengge R., 2017, More than Enzymes That Make or Break Cyclic Di-GMP-Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli., MBio 8(5)

 [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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