RegulonDB RegulonDB 10.7: Gene Form
   

hokB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydcA mokB hokB yncP sokB terminator sokBp sokBp sokBp3 sokBp3 TSS_1805 TSS_1805

Gene      
Name: hokB    Texpresso search in the literature
Synonym(s): ECK1412, G0-9610, b4428, ydcB
Genome position(nucleotides): 1491922 <-- 1492071 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.33
External database links:  
ASAP:
ABE-0047283
ECHOBASE:
EB1222
PORTECO:
hokB
REGULONDB:
b4428
STRING:
511145.b4428
M3D: hokB
COLOMBOS: hokB
PortEco: hokB


Product      
Name: toxin HokB
Synonym(s): HokB, YdcB, small toxic membrane polypeptide
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 5.626
Isoelectric point: 8.507
Motif(s):
 
Type Positions Sequence
5 -> 27 PLVVCLLIICITILTFTLLTRQT
6 -> 46 LVVCLLIICITILTFTLLTRQTLYELRFRDGDKEVAALMAC

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.3 - cell killing
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
biological_process GO:0022611 - dormancy process
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay
[IFC] Inferred by functional complementation
[IMP] Inferred from mutant phenotype
Reference(s): [1] Faridani OR., et al., 2006
[2] Pedersen K., et al., 1999
[3] Schneider D., et al., 2000
[4] Verstraeten N., et al., 2015
[5] Wilmaerts D., et al., 2018
[6] Woods R., et al., 2006
External database links:  
ECOCYC:
MONOMER0-1604
ECOLIWIKI:
b4428
INTERPRO:
IPR000021
INTERPRO:
IPR018084
PFAM:
PF01848
PRIDE:
P77494
PRINTS:
PR00281
PRODOM:
PD005979
PROSITE:
PS00556
PROTEINMODELPORTAL:
P77494
REFSEQ:
YP_025301
UNIPROT:
P77494


Operon      
Name: hokB         
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_1805 1491888 forward nd [RS-EPT-CBR] [7]
  promoter sokBp3 1492116 forward Similarity to the consensus
Read more >
[ICWHO] [8]


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] Faridani OR., Nikravesh A., Pandey DP., Gerdes K., Good L., 2006, Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli., Nucleic Acids Res 34(20):5915-22

 [2] Pedersen K., Gerdes K., 1999, Multiple hok genes on the chromosome of Escherichia coli., Mol Microbiol 32(5):1090-102

 [3] Schneider D., Duperchy E., Coursange E., Lenski RE., Blot M., 2000, Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements., Genetics 156(2):477-88

 [4] Verstraeten N., Knapen WJ., Kint CI., Liebens V., Van den Bergh B., Dewachter L., Michiels JE., Fu Q., David CC., Fierro AC., Marchal K., Beirlant J., Versees W., Hofkens J., Jansen M., Fauvart M., Michiels J., 2015, Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance., Mol Cell 59(1):9-21

 [5] Wilmaerts D., Bayoumi M., Dewachter L., Knapen W., Mika JT., Hofkens J., Dedecker P., Maglia G., Verstraeten N., Michiels J., 2018, The Persistence-Inducing Toxin HokB Forms Dynamic Pores That Cause ATP Leakage., MBio 9(4)

 [6] Woods R., Schneider D., Winkworth CL., Riley MA., Lenski RE., 2006, Tests of parallel molecular evolution in a long-term experiment with Escherichia coli., Proc Natl Acad Sci U S A 103(24):9107-12

 [7] 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.

 [8] 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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