RegulonDB RegulonDB 11.1: Gene Form
   

ygdG gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sdaB fucO ygdG TSS_3115 TSS_3115 ygdGp2 ygdGp2

Gene      
Name: ygdG    Texpresso search in the literature
Synonym(s): ECK2793, EG12372, b2798, exo, xni
Genome position(nucleotides): 2931055 --> 2931810
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.78
External database links:  
ASAP:
 ABE-0009174
ECHOBASE:
 EB2275
ECOLIHUB:
 ygdG
OU-MICROARRAY:
 b2798
STRING:
 511145.b2798
COLOMBOS: ygdG


Product      
Name: flap endonuclease
Synonym(s): Exo, ExoIX, Xni, YgdG
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 28.166
Isoelectric point: 6.678
Motif(s):
 
Type Positions Sequence Comment
5 -> 150 LLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLD
67 -> 67 K UniProt: Strongly reduces flap endonuclease activity..
160 -> 249 VQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRL UniProt: 5'-3' exonuclease.
184 -> 189 GIGPKS UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0000287 - magnesium ion binding
GO:0030955 - potassium ion binding
GO:0017108 - 5'-flap endonuclease activity
GO:0048256 - flap endonuclease activity
biological_process GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0033567 - DNA replication, Okazaki fragment processing
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [1] Anstey-Gilbert CS., et al., 2013
[2] Sayers JR. 1994
External database links:  
ALPHAFOLD:
 P38506
DIP:
 DIP-11145N
ECOCYC:
 EG12372-MONOMER
ECOLIWIKI:
 b2798
INTERPRO:
 IPR036279
INTERPRO:
 IPR029060
INTERPRO:
 IPR020046
INTERPRO:
 IPR020045
INTERPRO:
 IPR008918
INTERPRO:
 IPR002421
INTERPRO:
 IPR038969
INTERPRO:
 IPR022895
MODBASE:
 P38506
PANTHER:
 PTHR42646
PDB:
 3ZDE
PDB:
 3ZDD
PDB:
 3ZDC
PDB:
 3ZDB
PDB:
 3ZDA
PDB:
 3ZD8
PDB:
 3ZD9
PFAM:
 PF02739
PFAM:
 PF01367
PRIDE:
 P38506
REFSEQ:
 NP_417278
SMART:
 SM00475
SMART:
 SM00279
SMR:
 P38506
UNIPROT:
 P38506


Operon      
Name: ygdG         
Operon arrangement:
Transcription unit        Promoter
ygdG


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 ygdGp2 2930873 forward nd [COMP-AINF] [3]
  promoter TSS_3115 2931034 forward nd [RS-EPT-CBR] [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Anstey-Gilbert CS., Hemsworth GR., Flemming CS., Hodskinson MR., Zhang J., Sedelnikova SE., Stillman TJ., Sayers JR., Artymiuk PJ., 2013, The structure of Escherichia coli ExoIX--implications for DNA binding and catalysis in flap endonucleases., Nucleic Acids Res 41(17):8357-67

 [2] Sayers JR., 1994, Computer aided identification of a potential 5'-3' exonuclease gene encoded by Escherichia coli., J Theor Biol 170(4):415-21

 [3] 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

 [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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