RegulonDB RegulonDB 10.9: Gene Form
   

pdeH gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhjG kdgK pdeH TSS_4134 TSS_4134 yhjHp yhjHp yhjGp yhjGp TSS_4133 (cluster) TSS_4133 (cluster)

Gene      
Name: pdeH    Texpresso search in the literature
Synonym(s): ECK3510, EG12252, b3525, yhjH
Genome position(nucleotides): 3678420 <-- 3679187 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.73
External database links:  
ASAP:
ABE-0011515
ECHOBASE:
EB2162
ECOLIHUB:
yhjH
OU-MICROARRAY:
b3525
STRING:
511145.b3525
COLOMBOS: pdeH


Product      
Name: c-di-GMP phosphodiesterase PdeH
Synonym(s): PdeH, YhjH
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 29.601
Isoelectric point: 6.364
Motif(s):
 
Type Positions Sequence
27 -> 242 QCERAYTWQPIYQTCGRLMAVELLTVVTHPLNPSQRLPPDRYFTEITVSHRMEVVKEQIDLLAQKADFFIEHGLLASVNIDGPTLIALRQQPKILRQIERLPWLRFELVEHIRLPKDSTFASMCEFGPLWLDDFGTGMANFSALSEVRYDYIKIARELFVMLRQSPEGRTLFSQLLHLMNRYCRGVIVEGVETPEEWRDVQNSPAFAAQGWFLSRP
13 -> 255 EASIESLQERRFWLQCERAYTWQPIYQTCGRLMAVELLTVVTHPLNPSQRLPPDRYFTEITVSHRMEVVKEQIDLLAQKADFFIEHGLLASVNIDGPTLIALRQQPKILRQIERLPWLRFELVEHIRLPKDSTFASMCEFGPLWLDDFGTGMANFSALSEVRYDYIKIARELFVMLRQSPEGRTLFSQLLHLMNRYCRGVIVEGVETPEEWRDVQNSPAFAAQGWFLSRPAPIETLNTAVLAL
48 -> 48 E

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016787 - hydrolase activity
GO:0000166 - nucleotide binding
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity
biological_process GO:1902021 - regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Reference(s): [1] Glebes TY., et al., 2015
[2] Paul K., et al., 2010
[3] Reinders A., et al., 2015
External database links:  
ECOCYC:
EG12252-MONOMER
ECOLIWIKI:
b3525
INTERPRO:
IPR035919
INTERPRO:
IPR001633
PFAM:
PF00563
PRIDE:
P37646
PROSITE:
PS50883
REFSEQ:
NP_417982
SMART:
SM00052
SMR:
P37646
UNIPROT:
P37646


Operon      
Name: pdeH         
Operon arrangement:
Transcription unit        Promoter
yhjH


Transcriptional Regulation      
Display Regulation             
Activated by: FlhDC


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_4133 (cluster) 3678380 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [4]
  promoter TSS_4134 3679392 forward nd [RS-EPT-CBR] [4]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Glebes TY., Sandoval NR., Gillis JH., Gill RT., 2015, Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli., Biotechnol Bioeng 112(1):129-40

 [2] Paul K., Nieto V., Carlquist WC., Blair DF., Harshey RM., 2010, The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism., Mol Cell 38(1):128-39

 [3] Reinders A., Hee CS., Ozaki S., Mazur A., Boehm A., Schirmer T., Jenal U., 2015, Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli., J Bacteriol 198(3):448-62

 [4] 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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