RegulonDB RegulonDB 10.8: Gene Form
   

rpnD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yjiR mdtM rpnD TSS_5146 TSS_5146

Gene      
Name: rpnD    Texpresso search in the literature
Synonym(s): ECK4329, ECK4330, G7934, b4338, b4339, b4584, yjiP, yjiQ
Type: Pseudo Gene
Genome position(nucleotides): 4568998 --> 4569918 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.86
External database links:  
ASAP:
 ABE-0014227
ASAP:
 ABE-0014229
ASAP:
 ABE-0285116
ECHOBASE:
 EB2465
ECHOBASE:
 EB4384
ECOLIWIKI:
 b4339
ECOO157CYC:
 Z5940
OU-MICROARRAY:
 b4338
OU-MICROARRAY:
 b4339
PortEco:
 yjiQ
PortEco:
 yjiP
STRING:
 316407.85677081
UNIPROT:
 P0DP22
UNIPROT:
 B7NGZ6
COLOMBOS: rpnD


Product      
Name: putative inactive recombination-promoting nuclease-like protein RpnD
Sequence: Get amino acid sequence Fasta Format
Isoelectric point: 6.453
Motif(s):
 
Type Positions Sequence
1 -> 103 MTNFTTSTPHDALFKTFLTHPDTARDFMEIHLPKDLRELCDLDSLKLESASFVDEKLRALHSDILWSVKTREGDGYIYVVIEHQSREDIHMAFRLMRYSMAVM

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.4 - genetic exchange, recombination (for future)
Gene Ontology Terms (GO)  
biological_process GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
Reference(s): [1] Herzberg M., et al., 2006
External database links:  
ECOCYC:
 G7934-MONOMER
ECOLIWIKI:
 b4338
ECOO157CYC:
 Z5940-MONOMER
INTERPRO:
 IPR006842
INTERPRO:
 IPR010106
PFAM:
 PF04754
REFSEQ:
 NP_418758
UNIPROT:
 P0DP21


Operon      
Name: rpnD         
Operon arrangement:
Transcription unit        Promoter
 


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_5146 4569651 forward 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] Herzberg M., Kaye IK., Peti W., Wood TK., 2006, YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport., J Bacteriol 188(2):587-98

 [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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