RegulonDB RegulonDB 11.2: Gene Form
   

pdeN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yejA pdeN mepS terminator anti-terminator anti-anti-terminator TSS_2476 TSS_2476 TSS_2475 TSS_2475 yejAp yejAp rtnp1 rtnp1

Gene      
Name: pdeN    Texpresso search in the literature
Synonym(s): ECK2170, G7148, b2176, rtn
Genome position(nucleotides): 2270726 --> 2272282
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.55
External database links:  
ASAP:
 ABE-0007203
ECHOBASE:
 EB3830
ECOLIHUB:
 rtn
OU-MICROARRAY:
 b2176
STRING:
 511145.b2176
COLOMBOS: pdeN


Product      
Name: putative c-di-GMP phosphodiesterase PdeN
Synonym(s): PdeN, Rtn
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol,periplasmic space
Molecular weight: 58.588
Isoelectric point: 6.198
Motif(s):
 
Type Positions Sequence Comment
16 -> 36 CIVAGVMIAILVSCLQFLVAW UniProt: Helical.
42 -> 239 KYDTLITDVQKYLDTYFADLKSTTDRLQPLTLDTCQQANPELTARAAFSMNVRTFVLVKDKKTFCSSATGEMDIPLNELIPALDINKNVDMAILPGTPMVPNKPAIVIWYRNPLLKNSGVFAALNLNLTPSLFYSSRQEDYDGVALIIGNTALSTFSSRLMNVNELTDMPVRETKIAGIPLTVRLYADDWTWNDVWYA
236 -> 256 VWYAFLLGGMSGTVVGLLCYY UniProt: Helical.
261 -> 514 RMRPGREIMTAIKREQFYVAYQPVVDTQALRVTGLEVLLRWRHPVAGEIPPDAFINFAESQKMIVPLTQHLFELIARDAAELEKVLPVGVKFGINIAPDHLHSESFKADIQKLLTSLPAHHFQIVLEITERDMLKEQEATQLFAWLHSVGVEIAIDDFGTGHSALIYLERFTLDYLKIDRGFINAIGTETITSPVLDAVLTLAKRLNMLTVAEGVETPEQARWLSERGVNFMQGYWISRPLPLDDFVRWLKKPY UniProt: EAL.
267 -> 500 EIMTAIKREQFYVAYQPVVDTQALRVTGLEVLLRWRHPVAGEIPPDAFINFAESQKMIVPLTQHLFELIARDAAELEKVLPVGVKFGINIAPDHLHSESFKADIQKLLTSLPAHHFQIVLEITERDMLKEQEATQLFAWLHSVGVEIAIDDFGTGHSALIYLERFTLDYLKIDRGFINAIGTETITSPVLDAVLTLAKRLNMLTVAEGVETPEQARWLSERGVNFMQGYWISRP

 
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:
 P76446
DIP:
 DIP-10813N
ECOCYC:
 G7148-MONOMER
ECOLIWIKI:
 b2176
INTERPRO:
 IPR024744
INTERPRO:
 IPR001633
INTERPRO:
 IPR035919
PFAM:
 PF00563
PFAM:
 PF12792
PRIDE:
 P76446
PRODB:
 PRO_000023894
PROSITE:
 PS50883
REFSEQ:
 NP_416681
SMART:
 SM00052
SMR:
 P76446
UNIPROT:
 P76446


Operon      
Name: pdeN         
Operon arrangement:
Transcription unit        Promoter
pdeN


RNA cis-regulatory element    
Attenuation: Transcriptional


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 rtnp1 2270678 forward nd [COMP-AINF] [2]
  promoter yejAp 2272312 forward nd [COMP-AINF], [COMP-AINF-POSITIONAL-IDENTIFICATION] [2]
  promoter TSS_2475 2272388 forward nd [RS-EPT-CBR] [3]
  promoter TSS_2476 2273514 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [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] 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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