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UniProtKB - P0AFX0 (HPF_ECOLI)

Entry version 103 (13 Nov 2019)
Sequence version 1 (20 Dec 2005)
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Protein

Ribosome hibernation promoting factor

Gene

hpf

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

Annotation score:4 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

During stationary phase, promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes (PubMed:18174192). Converts immature 90S particles formed by RMF into 100S ribosomes (PubMed:16324148). Crystallization with T.thermophilus 70S ribosomes shows it binds in the channel between the head and body of the 30S subunit, where mRNA, tRNAs, initiation factors IF1 and IF3 and elongation factor G would bind; however RMF is still able to bind (PubMed:22605777). In this crystal binding of HPF induces movement of the 30S head domain away from the rest of the ribosome, presumably so they would more easily form dimers (PubMed:22605777). May also function as a potential translational inhibitor (PubMed:18174192).5 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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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

Biological processTranslation regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11681-MONOMER
ECOL316407:JW3170-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:
Ribosome hibernation promoting factor1 Publication
Short name:
HPF1 Publication
Alternative name(s):
Hibernation factor HPF1 Publication
<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:hpf1 Publication
Synonyms:yhbH
Ordered Locus Names:b3203, JW3170
<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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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

Complete GO annotation on QuickGO ...

<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

Non-essential gene, no formation of inactive 100S ribosomes. Double hpf-yfiA deletion mutants form 90S ribosomes (PubMed:16324148). A quadruple yfiA-hpf-rmf-sra knockout strain is significantly outcompeted by wild-type after 4 days growth (PubMed:17277072). No change in sensitivity to aminoglycoside antiobiotic gentamicin in stationary phase cultures (PubMed:26324267).3 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 ‘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_00000974171 – 95Ribosome hibernation promoting factorAdd BLAST95

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0AFX0

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

More...PaxDbi		P0AFX0

PRoteomics IDEntifications database

More...PRIDEi		P0AFX0

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced during stationary growth phase (at protein level) (PubMed:11168583). Induced by the signal autoinducer AI-2 (PubMed:11514505).2 Publications

<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

Associates exclusively with 100S ribosomes, which are dimers of 70S ribosomes.

2 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
P0A9882EBI-561113,EBI-542385

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4259283, 29 interactors

Database of interacting proteins

More...DIPi		DIP-48273N

Protein interaction database and analysis system

More...IntActi		P0AFX0, 4 interactors

STRING: functional protein association networks

More...STRINGi		511145.b3203

<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

195
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		P0AFX0

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		P0AFX0

<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 HPF/YfiA ribosome-associated protein family. Short HPF subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG41080QH Bacteria
COG1544 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000264773

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0AFX0

KEGG Orthology (KO)

More...KOi		K05808

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0AFX0

Family and domain databases

Conserved Domains Database

More...CDDi		cd00552 RaiA, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.160.100, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR036567 RHF-like
IPR003489 RHF/RaiA

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02482 Ribosomal_S30AE, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF69754 SSF69754, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00741 yfiA, 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.

P0AFX0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQLNITGNNV EITEALREFV TAKFAKLEQY FDRINQVYVV LKVEKVTHTS 
        60         70         80         90 
DATLHVNGGE IHASAEGQDM YAAIDGLIDK LARQLTKHKD KLKQH
Length:95
Mass (Da):10,750
Last modified:December 20, 2005 - v1
<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:i5B8F737E6E3A91AE
GO

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
D12938 Genomic DNA Translation: BAA02316.1
Z27094 Genomic DNA Translation: CAA81618.1
U12684 Genomic DNA Translation: AAB60164.1
U18997 Genomic DNA Translation: AAA58005.1
U00096 Genomic DNA Translation: AAC76235.1
AP009048 Genomic DNA Translation: BAE77247.1

Protein sequence database of the Protein Information Resource

More...PIRi		I76719

NCBI Reference Sequences

More...RefSeqi		NP_417670.1, NC_000913.3
WP_001176599.1, NZ_STEB01000012.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC76235; AAC76235; b3203
BAE77247; BAE77247; BAE77247

Database of genes from NCBI RefSeq genomes

More...GeneIDi		947718

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW3170
eco:b3203

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3528

<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
D12938 Genomic DNA Translation: BAA02316.1
Z27094 Genomic DNA Translation: CAA81618.1
U12684 Genomic DNA Translation: AAB60164.1
U18997 Genomic DNA Translation: AAA58005.1
U00096 Genomic DNA Translation: AAC76235.1
AP009048 Genomic DNA Translation: BAE77247.1
PIRiI76719
RefSeqiNP_417670.1, NC_000913.3
WP_001176599.1, NZ_STEB01000012.1

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
2RQLNMR-A1-95[»]
4V8HX-ray3.10AX/CX1-95[»]
6H4Nelectron microscopy3.00x1-95[»]
6H58electron microscopy7.90x/xx1-95[»]
SMRiP0AFX0
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4259283, 29 interactors
DIPiDIP-48273N
IntActiP0AFX0, 4 interactors
STRINGi511145.b3203

Proteomic databases

jPOSTiP0AFX0
PaxDbiP0AFX0
PRIDEiP0AFX0

Genome annotation databases

EnsemblBacteriaiAAC76235; AAC76235; b3203
BAE77247; BAE77247; BAE77247
GeneIDi947718
KEGGiecj:JW3170
eco:b3203
PATRICifig|1411691.4.peg.3528

Organism-specific databases

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

More...EchoBASEi		EB1632

Phylogenomic databases

eggNOGiENOG41080QH Bacteria
COG1544 LUCA
HOGENOMiHOG000264773
InParanoidiP0AFX0
KOiK05808
PhylomeDBiP0AFX0

Enzyme and pathway databases

BioCyciEcoCyc:EG11681-MONOMER
ECOL316407:JW3170-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AFX0

Protein Ontology

More...PROi		PR:P0AFX0

Family and domain databases

CDDicd00552 RaiA, 1 hit
Gene3Di3.30.160.100, 1 hit
InterProiView protein in InterPro
IPR036567 RHF-like
IPR003489 RHF/RaiA
PfamiView protein in Pfam
PF02482 Ribosomal_S30AE, 1 hit
SUPFAMiSSF69754 SSF69754, 1 hit
TIGRFAMsiTIGR00741 yfiA, 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 nameiHPF_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: P0AFX0
Secondary accession number(s): P31221, Q2M909
<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: December 20, 2005
Last sequence update: December 20, 2005
Last modified: November 13, 2019
This is version 103 of the entry and version 1 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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