RegulonDB RegulonDB 10.8: Gene Form
   

rnlB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rnlA yfjP rnlB yfjM IscR anti-terminator anti-anti-terminator terminator anti-anti-terminator anti-terminator yfjPp6 yfjPp6 yfjPp5 yfjPp5 yfjPp8 yfjPp8 TSS_2981 TSS_2981 rnlBp2 rnlBp2 TSS_2980 TSS_2980 rnlBp rnlBp yfjMp3 yfjMp3 rnlAp rnlAp TSS_2978 TSS_2978 TSS_2977 TSS_2977 rnlAp2 rnlAp2

Gene      
Name: rnlB    Texpresso search in the literature
Synonym(s): ECK2627, G7366, b2631, yfjO
Genome position(nucleotides): 2766984 --> 2767355 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
45.97
External database links:  
ASAP:
ABE-0008665
ECHOBASE:
EB2993
OU-MICROARRAY:
b2631
PortEco:
yfjO
STRING:
511145.b2631
COLOMBOS: rnlB


Product      
Name: CP4-57 prophage; antitoxin RnlB
Synonym(s): CP4-57 prophage, antitoxin of the RnlA-RnlB toxin-antitoxin system, RnlB, YfjO
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 13.665
Isoelectric point: 4.24
Motif(s):
 
Type Positions Sequence
14 -> 111 KAVVMATGFENPLSSVNEIETKLSALLGSETTGEILFDLLCANGPEWNRFVTLEMKYGRIMLDTAKIIDEQDVPTHILSKLTFTLRNHPEYLEASVLS

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.3 - cell killing
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
biological_process GO:0060702 - negative regulation of endoribonuclease activity
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Koga M., et al., 2011
[2] Naka K., et al., 2017
[3] Tsukuda M., et al., 2015
External database links:  
ECOCYC:
G7366-MONOMER
ECOLIWIKI:
b2631
INTERPRO:
IPR031834
PFAM:
PF15933
PRIDE:
P52130
REFSEQ:
NP_417120
UNIPROT:
P52130


Operon      
Name: rnlAB         
Operon arrangement:
Transcription unit        Promoter
rnlAB
rnlA
rnlB
rnlB


Transcriptional Regulation      
Display Regulation             
Repressed by: IscR


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_2977 2765896 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2978 2765900 forward nd [RS-EPT-CBR] [4]
  promoter yfjMp3 2765985 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_2980 2766837 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2981 2767514 reverse nd [RS-EPT-CBR] [4]
  promoter yfjPp8 2767540 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yfjPp5 2767642 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yfjPp6 2767644 forward Similarity to the consensus
Read more >
[ICWHO] [5]


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] Koga M., Otsuka Y., Lemire S., Yonesaki T., 2011, Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system., Genetics 187(1):123-30

 [2] Naka K., Qi D., Yonesaki T., Otsuka Y., 2017, RnlB Antitoxin of the Escherichia coli RnlA-RnlB Toxin-Antitoxin Module Requires RNase HI for Inhibition of RnlA Toxin Activity., Toxins (Basel) 9(1)

 [3] Tsukuda M., Nakashima N., Miyazaki K., 2015, Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli., J Biosci Bioeng 120(5):591-5

 [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.

 [5] 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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