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Entry version 137 (13 Nov 2019)
Sequence version 2 (23 Jan 2007)
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Protein

RNA-binding protein Hfq

Gene

hfq

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32 (PubMed:17158661). Binds with high specificity to tRNAs (PubMed:18230766). Binds sRNA antitoxin RalA (PubMed:24748661). In vitro, stimulates synthesis of long tails by poly(A) polymerase I (PubMed:10677490). Required for RNA phage Qbeta replication (PubMed:805130). Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation (PubMed:19909729).6 Publications

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, RNA-binding
Biological processStress response

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG10438-MONOMER
ECOL316407:JW4130-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
RNA-binding protein HfqUniRule annotation
Alternative name(s):
HF-1
Host factor-I protein
Short name:
HF-I
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:hfqUniRule annotation
Ordered Locus Names:b4172, JW4130
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Deletion of hfq seems to lead to a significant translational fidelity problem. Deletion increases persister cell formation (PubMed:19909729). Deletion abolishes the antitoxin activity of sRNA antitoxin RalA, preventing it from neutralizing toxin RalR (PubMed:24748661).2 Publications

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved3 Publications
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000956012 – 102RNA-binding protein HfqAdd BLAST101

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
P0A6X3

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P0A6X3

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P0A6X3

PRoteomics IDEntifications database

More...
PRIDEi
P0A6X3

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homohexamer (PubMed:12853626).

Interacts with H-NS (PubMed:11222598).

UniRule annotation2 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
P0AG305EBI-547637,EBI-545468

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4261250, 265 interactors

Database of interacting proteins

More...
DIPi
DIP-36047N

Protein interaction database and analysis system

More...
IntActi
P0A6X3, 78 interactors

Molecular INTeraction database

More...
MINTi
P0A6X3

STRING: functional protein association networks

More...
STRINGi
511145.b4172

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1102
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P0A6X3

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0A6X3

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the Hfq family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105KW8 Bacteria
COG1923 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000004931

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0A6X3

KEGG Orthology (KO)

More...
KOi
K03666

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0A6X3

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01716 Hfq, 1 hit

Database of protein disorder

More...
DisProti
DP01050

HAMAP database of protein families

More...
HAMAPi
MF_00436 Hfq, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR005001 Hfq
IPR010920 LSM_dom_sf

The PANTHER Classification System

More...
PANTHERi
PTHR34772 PTHR34772, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF17209 Hfq, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50182 SSF50182, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02383 Hfq, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P0A6X3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV
60 70 80 90 100
SQMVYKHAIS TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE

TE
Length:102
Mass (Da):11,166
Last modified:January 23, 2007 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iE47FA9B07A39304D
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA24175 differs from that shown. Reason: Frameshift.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D00743 Genomic DNA Translation: BAA00644.1
U14003 Genomic DNA Translation: AAA97068.1
U00096 Genomic DNA Translation: AAC77129.1
AP009048 Genomic DNA Translation: BAE78173.1
M63655 Genomic DNA Translation: AAA24175.1 Frameshift.
U00005 Unassigned DNA Translation: AAC43397.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S26832 S56397

NCBI Reference Sequences

More...
RefSeqi
NP_418593.1, NC_000913.3
WP_001051883.1, NZ_STEB01000013.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC77129; AAC77129; b4172
BAE78173; BAE78173; BAE78173

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
948689

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW4130
eco:b4172

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.2529

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00743 Genomic DNA Translation: BAA00644.1
U14003 Genomic DNA Translation: AAA97068.1
U00096 Genomic DNA Translation: AAC77129.1
AP009048 Genomic DNA Translation: BAE78173.1
M63655 Genomic DNA Translation: AAA24175.1 Frameshift.
U00005 Unassigned DNA Translation: AAC43397.1
PIRiS26832 S56397
RefSeqiNP_418593.1, NC_000913.3
WP_001051883.1, NZ_STEB01000013.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HK9X-ray2.15A/B/C/D/E/F1-72[»]
1M7Cmodel-A/B/C/D/E/F9-76[»]
1OOUmodel-A/B/C/D/E/F6-64[»]
1OOVmodel-A/B/C/D/E/F6-64[»]
2Y90X-ray2.25A1-102[»]
2YHTX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L1-72[»]
3GIBX-ray2.40A/B/C2-69[»]
3QHSX-ray2.85A/B/C/D/E/F/G/H/I/J/K/L1-102[»]
3QO3X-ray2.15A/B/C/D/E/F1-65[»]
3RERX-ray1.70A/B/C/D/E/F1-65[»]
3RESX-ray2.00A/B/C/D/E/F/G/H/I/J/K/L1-65[»]
3VU3X-ray2.85C/D/E/F/G/H1-102[»]
4JRIX-ray1.83A/B/C/D2-69[»]
4JRKX-ray1.89A/B/C2-69[»]
4JUVX-ray2.19A/B/C/D/E/F2-69[»]
4RCBX-ray1.63A5-71[»]
4RCCX-ray1.98A5-71[»]
4V2SX-ray3.48A/B/C/D/E/F1-102[»]
5UK7X-ray3.00A/B/C/D/E/F/G/H/I/J/K/L2-69[»]
SMRiP0A6X3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261250, 265 interactors
DIPiDIP-36047N
IntActiP0A6X3, 78 interactors
MINTiP0A6X3
STRINGi511145.b4172

Proteomic databases

EPDiP0A6X3
jPOSTiP0A6X3
PaxDbiP0A6X3
PRIDEiP0A6X3

Genome annotation databases

EnsemblBacteriaiAAC77129; AAC77129; b4172
BAE78173; BAE78173; BAE78173
GeneIDi948689
KEGGiecj:JW4130
eco:b4172
PATRICifig|1411691.4.peg.2529

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB0433

Phylogenomic databases

eggNOGiENOG4105KW8 Bacteria
COG1923 LUCA
HOGENOMiHOG000004931
InParanoidiP0A6X3
KOiK03666
PhylomeDBiP0A6X3

Enzyme and pathway databases

BioCyciEcoCyc:EG10438-MONOMER
ECOL316407:JW4130-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0A6X3

Protein Ontology

More...
PROi
PR:P0A6X3

Family and domain databases

CDDicd01716 Hfq, 1 hit
DisProtiDP01050
HAMAPiMF_00436 Hfq, 1 hit
InterProiView protein in InterPro
IPR005001 Hfq
IPR010920 LSM_dom_sf
PANTHERiPTHR34772 PTHR34772, 1 hit
PfamiView protein in Pfam
PF17209 Hfq, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit
TIGRFAMsiTIGR02383 Hfq, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHFQ_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0A6X3
Secondary accession number(s): O24728
, P25521, Q2M6D3, Q47383
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: November 13, 2019
This is version 137 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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