RegulonDB RegulonDB 10.8: Gene Form
   

yajD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

secF tsx yajD terminator anti-terminator anti-anti-terminator TSS_524 TSS_524 yajDp5 yajDp5 yajDp6 yajDp6 TSS_523 (cluster) TSS_523 (cluster) TSS_522 TSS_522 TSS_521 TSS_521 TSS_520 (cluster) TSS_520 (cluster) TSS_519 TSS_519 TSS_518 TSS_518

Gene      
Name: yajD    Texpresso search in the literature
Synonym(s): ECK0404, EG11097, b0410
Genome position(nucleotides): 430605 --> 430952 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.13
External database links:  
ASAP:
ABE-0001422
ECHOBASE:
EB1089
OU-MICROARRAY:
b0410
PortEco:
yajD
STRING:
511145.b0410
COLOMBOS: yajD


Product      
Name: HNH nuclease family protein YajD
Synonym(s): YajD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 13.364
Isoelectric point: 6.62
Motif(s):
 
Type Positions Sequence
109 -> 115 AMMNKKK
27 -> 75 CGRCSREFVYSNLRELTVHHIDHDHTNNPEDGSNWELLCLYCHDHEHSK

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
biological_process GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG11097-MONOMER
ECOLIWIKI:
b0410
INTERPRO:
IPR002711
INTERPRO:
IPR003615
PFAM:
PF01844
PRIDE:
P0AAQ2
REFSEQ:
NP_414944
SMART:
SM00507
UNIPROT:
P0AAQ2


Operon      
Name: yajD         
Operon arrangement:
Transcription unit        Promoter
 


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 TSS_518 429682 forward nd [RS-EPT-CBR] [1]
  promoter TSS_519 430048 forward nd [RS-EPT-CBR] [1]
  promoter TSS_520 (cluster) 430051 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_521 430054 forward nd [RS-EPT-CBR] [1]
  promoter TSS_522 430059 forward nd [RS-EPT-CBR] [1]
  promoter TSS_523 (cluster) 430063 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter yajDp6 430469 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yajDp5 430530 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_524 432002 reverse nd [RS-EPT-CBR] [1]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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


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