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Entry version 115 (08 May 2019)
Sequence version 2 (01 Feb 1995)
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Protein

Ribosome hibernation promotion factor

Gene

yvyD

Organism
Bacillus subtilis (strain 168)
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

Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth. May not be the only factor implicated (PubMed:22950019). Might negatively regulate the activity of the sigma-54 factor (SigL) (PubMed:9852014).UniRule annotation2 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

Biological processStress response, Translation regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU35310-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 promotion factorUniRule annotation
Short name:
HPFUniRule annotation
Alternative name(s):
Hst231 Publication
Putative sigma-54 modulation protein
SigL modulation protein
<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:yvyD
Synonyms:hpfUniRule annotation, yviI
Ordered Locus Names:BSU35310
ORF Names:orf189
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<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
  • UP000001570 <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

<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

Keywords - Cellular componenti

Cytoplasm

<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

The expression of a sigL-dependent gene (levD) is up-regulated two-fold in cells lacking yvyD, but the relative amount of the sigL transcript is not increased (PubMed:9852014). In cells overexpressing ppGpp synthase YwaC, deletion of this gene causes loss of 100S ribosome formation by dimerizing 70S ribosomes (PubMed:22950019).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 ‘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_00002085891 – 189Ribosome hibernation promotion factorAdd BLAST189

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
P28368

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

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PaxDbi
P28368

PRoteomics IDEntifications database

More...
PRIDEi
P28368

<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

Expressed under the dual control of sigma-B (PubMed:9296790) and sigma-H factors (PubMed:9296790, PubMed:9852014). The sigma-B-dependent promoter drives expression of yvyD under stress conditions and after glucose starvation, whereas a sigma-H-dependent promoter is responsible for yvyD transcription following amino acid depletion (PubMed:9852014). Also claimed to be under sole control of sigma-H (PubMed:22950019).3 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

Interacts with 100S ribosomes. Not associated with 70S ribosome monomers, about 1 monomer per ribosome (PubMed:22950019).

UniRule annotation1 Publication

Protein-protein interaction databases

Protein interaction database and analysis system

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IntActi
P28368, 1 interactor

Molecular INTeraction database

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MINTi
P28368

STRING: functional protein association networks

More...
STRINGi
224308.BSU35310

<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

3D structure databases

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

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SMRi
P28368

Database of comparative protein structure models

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ModBasei
Search...

<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. Long HPF subfamily.UniRule annotation1 Publication

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105MS2 Bacteria
COG1544 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000074927

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P28368

Identification of Orthologs from Complete Genome Data

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OMAi
HGGYGVI

Database for complete collections of gene phylogenies

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PhylomeDBi
P28368

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00552 RaiA, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.30.160.100, 1 hit
3.30.505.50, 1 hit

HAMAP database of protein families

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HAMAPi
MF_00839 HPF, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR034694 HPF_long/plastid
IPR036567 RHF-like
IPR003489 RHF/RaiA
IPR032528 Ribosom_S30AE_C
IPR038416 Ribosom_S30AE_C_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF16321 Ribosom_S30AE_C, 1 hit
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.

P28368-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNYNIRGENI EVTPALKDHV ERKIGKLERY FDHSVDADVN VNLKFYNDKE
60 70 80 90 100
SKVEVTIPMT DLALRSEVHN EDMYNAIDLA TNKLERQIRK HKTKVNRKFR
110 120 130 140 150
EQGSPKYLLA NGLGSDTDIA VQDDIEEEES LDIVRQKRFN LKPMDSEEAI
160 170 180
LQMNMLGHNF FVFTNAETNL TNVVYRRNDG KYGLIEPTE
Length:189
Mass (Da):21,980
Last modified:February 1, 1995 - 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:iA015EA9095C9CFA3
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
Z31376 Genomic DNA Translation: CAA83251.1
U56901 Genomic DNA Translation: AAC44956.1
AL009126 Genomic DNA Translation: CAB15548.1
D10279 Genomic DNA Translation: BAA01121.1

Protein sequence database of the Protein Information Resource

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PIRi
I40400

NCBI Reference Sequences

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RefSeqi
NP_391411.1, NC_000964.3
WP_003228031.1, NZ_JNCM01000033.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB15548; CAB15548; BSU35310

Database of genes from NCBI RefSeq genomes

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GeneIDi
936715

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU35310

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.3821

<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
Z31376 Genomic DNA Translation: CAA83251.1
U56901 Genomic DNA Translation: AAC44956.1
AL009126 Genomic DNA Translation: CAB15548.1
D10279 Genomic DNA Translation: BAA01121.1
PIRiI40400
RefSeqiNP_391411.1, NC_000964.3
WP_003228031.1, NZ_JNCM01000033.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5NJTelectron microscopy3.80x1-104[»]
SMRiP28368
ModBaseiSearch...

Protein-protein interaction databases

IntActiP28368, 1 interactor
MINTiP28368
STRINGi224308.BSU35310

Proteomic databases

jPOSTiP28368
PaxDbiP28368
PRIDEiP28368

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15548; CAB15548; BSU35310
GeneIDi936715
KEGGibsu:BSU35310
PATRICifig|224308.179.peg.3821

Phylogenomic databases

eggNOGiENOG4105MS2 Bacteria
COG1544 LUCA
HOGENOMiHOG000074927
InParanoidiP28368
OMAiHGGYGVI
PhylomeDBiP28368

Enzyme and pathway databases

BioCyciBSUB:BSU35310-MONOMER

Family and domain databases

CDDicd00552 RaiA, 1 hit
Gene3Di3.30.160.100, 1 hit
3.30.505.50, 1 hit
HAMAPiMF_00839 HPF, 1 hit
InterProiView protein in InterPro
IPR034694 HPF_long/plastid
IPR036567 RHF-like
IPR003489 RHF/RaiA
IPR032528 Ribosom_S30AE_C
IPR038416 Ribosom_S30AE_C_sf
PfamiView protein in Pfam
PF16321 Ribosom_S30AE_C, 1 hit
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_BACSU
<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: P28368
<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 1, 1992
Last sequence update: February 1, 1995
Last modified: May 8, 2019
This is version 115 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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