RegulonDB RegulonDB 10.9: Gene Form
   

hfq gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hflX miaA hfq mutL CRP TSS_5023 TSS_5023 TSS_5022 TSS_5022 TSS_5021 TSS_5021 TSS_5020 TSS_5020 TSS_5019 TSS_5019 TSS_5018 TSS_5018 TSS_5017 (cluster) TSS_5017 (cluster) TSS_5016 TSS_5016 hfqp3 hfqp3 hfqp2 hfqp2

Gene      
Name: hfq    Texpresso search in the literature
Synonym(s): ECK4168, EG10438, b4172
Genome position(nucleotides): 4400288 --> 4400596 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.87
External database links:  
ASAP:
ABE-0013659
CGSC:
34450
ECHOBASE:
EB0433
ECOLIHUB:
hfq
OU-MICROARRAY:
b4172
STRING:
511145.b4172
COLOMBOS: hfq


Product      
Name: RNA-binding protein Hfq
Synonym(s): HF-I, Hfq, host factor I
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 11.166
Isoelectric point: 7.907
Motif(s):
 
Type Positions Sequence
7 -> 69 LQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS
2 -> 102 AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.4 - global
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0003681 - bent DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045974 - regulation of translation, ncRNA-mediated
GO:0040033 - negative regulation of translation, ncRNA-mediated
GO:0043487 - regulation of RNA stability
GO:0045975 - positive regulation of translation, ncRNA-mediated
Note(s): Note(s): ...[more].
Reference(s): [1] Ruiz N., et al., 2003
[2] Sharan M., et al., 2017
External database links:  
DIP:
DIP-36047N
DISPROT:
DP01050
ECOCYC:
EG10438-MONOMER
ECOLIWIKI:
b4172
INTERPRO:
IPR010920
INTERPRO:
IPR005001
MINT:
P0A6X3
PANTHER:
PTHR34772
PDB:
3RER
PDB:
3RES
PDB:
3VU3
PDB:
4JRI
PDB:
4JRK
PDB:
4JUV
PDB:
4RCB
PDB:
4RCC
PDB:
4V2S
PDB:
5UK7
PDB:
3QO3
PDB:
3QHS
PDB:
3GIB
PDB:
2YHT
PDB:
2Y90
PDB:
1OOV
PDB:
1OOU
PDB:
1M7C
PDB:
1HK9
PFAM:
PF17209
PRIDE:
P0A6X3
PRODB:
PRO_000022886
REFSEQ:
NP_418593
SMR:
P0A6X3
UNIPROT:
P0A6X3


Operon      
Name: nnr-tsaE-amiB-mutL-miaA-hfq-hflXKC         
Operon arrangement:
Transcription unit        Promoter
yjeFE-amiB-mutL-miaA-hfq-hflXKC
yjeFE-amiB-mutL-miaA-hfq-hflXKC
yjeFE-amiB-mutL-miaA-hfq-hflXKC
mutL-miaA-hfq-hflXKC
mutL-miaA-hfq-hflXKC
miaA-hfq-hflXKC
miaA-hfq-hflXKC
hfq-hflXKC
hfq-hflXKC
hfq-hflXKC
tsaE-amiB-mutL-miaA-hfq-hflXKC


Transcriptional Regulation      
Display Regulation             
Repressed by: CRP


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_5016 4400234 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5017 (cluster) 4401549 forward For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_5018 4401552 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5019 4401621 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5020 4401731 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5021 4401841 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5022 4401847 forward nd [RS-EPT-CBR] [3]
  promoter TSS_5023 4401919 forward nd [RS-EPT-CBR] [3]


Evidence    

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



Reference(s)    

 [1] Ruiz N., Silhavy TJ., 2003, Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion., J Bacteriol 185(20):5984-92

 [2] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96

 [3] 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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