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Entry version 109 (12 Aug 2020)
Sequence version 2 (23 Jan 2007)
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Protein

SsrA-binding protein

Gene

smpB

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

Required for rescue of stalled ribosomes mediated by trans-translation. Binds to tmRNA RNA (also known as SsrA or 10Sa RNA, 363 nucleotides in this organism), required for stable binding of tmRNA to ribosomes (PubMed:10393194, PubMed:11904185, PubMed:11917023). tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB (Probable). tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. Able to recruit charged tmRNA to ribosomes (PubMed:15069072). Does not play a role in transcription, processing or Ala-aminoacylation of tmRNA (PubMed:10393194). Other studies have shown it stimulates aminoacylation of tmRNA (PubMed:11917023, PubMed:11904185). May protect tmRNA from degradation (PubMed:11917023). Binds to tmRNA that cannot be aminoacylated (tmRNA G3A), does not bind to tmRNA mutations near the tRNA-like termini (tmRNA G19C, A334U); other tmRNA mutations that block trans-translation still bind SmpB (PubMed:11917023). With tmRNA may play a role in bacterial persistence (PubMed:23812681). During trans-translation Ala-aminoacylated transfer-messenger RNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA, the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.1 Publication9 Publications

Miscellaneous

Although the Fu et al., electron microscopy paper indicates this protein came from E.coli its sequence maps to T.thermophilus (PubMed:20940705). The same situation holds for Ramrath et al., (PubMed:22622583).2 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

  • RNA binding Source: EcoCyc

GO - Biological processi

  • trans-translation Source: UniProtKB-UniRule
  • trans-translation-dependent protein tagging Source: EcoCyc

<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 functionRNA-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11782-MONOMER
ECOL316407:JW2601-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%5Fand%5Ftaxonomy%5Fsection">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:
SsrA-binding proteinUniRule annotation
Alternative name(s):
Small protein BUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:smpBUniRule annotation
Synonyms:smqB
Ordered Locus Names:b2620, JW2601
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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

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

No visible phenotype during growth on solid medium at 16-42 degrees Celsius on rich or minimal media, no peptide-tagging of proteins translated from mRNA lacking a stop codon by tmRNA, i.e. no trans-translation (PubMed:10393194, PubMed:11917023, PubMed:15069072). 4-8 fold increased susceptibility to a number of antibiotics (norfloxacin, gentamicin, trimethoprim, tetracycline and streptomycin but not ampicillin), very significantly reduced production of persister cells (PubMed:23812681). A number of bacteriophage development defects (PubMed:10393194).4 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi137 – 139DKR → AAA: Almost complete loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication3
Mutagenesisi138 – 139KR → AA: About half loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication2
Mutagenesisi139R → E: About half loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication1
Mutagenesisi140 – 160Missing : Complete loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 PublicationAdd BLAST21
Mutagenesisi147W → C or D: 70% loss of tagging by trans-translation, binds tmRNA normally. 1 Publication1
Mutagenesisi147W → K: 97% loss of tagging by trans-translation, binds tmRNA normally, altered binding of the tmRNA-SmpB complex in the ribosomes A-site. 1 Publication1
Mutagenesisi152 – 160Missing : Complete loss of protein tagging by trans-translation, binds ribosomes normally. 1 Publication9
Mutagenesisi154 – 160Missing : Almost complete loss of protein tagging by trans-translation, binds tmRNA normally. 1 Publication7
Mutagenesisi154 – 155IM → AA: Decreased protein tagging by trans-translation, binds ribosomes normally. 1 Publication2
Mutagenesisi154 – 155IM → DE: Loss of protein tagging by trans-translation, binds tmRNA and ribosomes normally. 1 Publication2
Mutagenesisi154 – 155IM → LI, RK or QQ: No effect on protein tagging by trans-translation. 1 Publication2
Mutagenesisi155 – 160Missing : Slightly increased protein tagging by trans-translation, binds ribosomes normally. 1 Publication6
Mutagenesisi156 – 160Missing : No effect on protein tagging by trans-translation, binds ribosomes normally. 1 Publication5

<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%5Fprocessing%5Fsection">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 methionineiRemoved2 Publications
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001029442 – 160SsrA-binding proteinAdd BLAST159

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P0A832

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

More...
PaxDbi
P0A832

PRoteomics IDEntifications database

More...
PRIDEi
P0A832

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Binds tmRNA (PubMed:10393194, PubMed:11904185, PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583). The SmpB-tmRNA complex binds to stalled ribosomes (PubMed:10393194, PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583).

7 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4260987, 42 interactors
851624, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-47871N

Protein interaction database and analysis system

More...
IntActi
P0A832, 32 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2620

<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

More...
SMRi
P0A832

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
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 SmpB family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0691, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_108953_3_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0A832

KEGG Orthology (KO)

More...
KOi
K03664

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0A832

Family and domain databases

Conserved Domains Database

More...
CDDi
cd09294, SmpB, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.280.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00023, SmpB, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR023620, SmpB
IPR000037, SsrA-bd_prot
IPR020081, SsrA-bd_prot_CS

The PANTHER Classification System

More...
PANTHERi
PTHR30308, PTHR30308, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01668, SmpB, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF74982, SSF74982, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00086, smpB, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01317, SSRP, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P0A832-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN
60 70 80 90 100
ISDSYVLLRD GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL
110 120 130 140 150
YGRVNREGYT VVALSLYWKN AWCKVKIGVA KGKKQHDKRS DIKEREWQVD
160
KARIMKNAHR
Length:160
Mass (Da):18,269
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:iF7E45A16540EA300
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D12501 Genomic DNA Translation: BAA02062.1
U36840 Genomic DNA Translation: AAA79790.1
U00096 Genomic DNA Translation: AAC75669.1
AP009048 Genomic DNA Translation: BAA16505.2

Protein sequence database of the Protein Information Resource

More...
PIRi
JS0701

NCBI Reference Sequences

More...
RefSeqi
NP_417110.1, NC_000913.3
WP_000162574.1, NZ_STEB01000040.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75669; AAC75669; b2620
BAA16505; BAA16505; BAA16505

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
52077893
947296

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2601
eco:b2620

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.4119

<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
D12501 Genomic DNA Translation: BAA02062.1
U36840 Genomic DNA Translation: AAA79790.1
U00096 Genomic DNA Translation: AAC75669.1
AP009048 Genomic DNA Translation: BAA16505.2
PIRiJS0701
RefSeqiNP_417110.1, NC_000913.3
WP_000162574.1, NZ_STEB01000040.1

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
6Q97electron microscopy3.90514-158[»]
6Q9Aelectron microscopy3.70514-131[»]
SMRiP0A832
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4260987, 42 interactors
851624, 1 interactor
DIPiDIP-47871N
IntActiP0A832, 32 interactors
STRINGi511145.b2620

Proteomic databases

jPOSTiP0A832
PaxDbiP0A832
PRIDEiP0A832

Genome annotation databases

EnsemblBacteriaiAAC75669; AAC75669; b2620
BAA16505; BAA16505; BAA16505
GeneIDi52077893
947296
KEGGiecj:JW2601
eco:b2620
PATRICifig|1411691.4.peg.4119

Organism-specific databases

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

More...
EchoBASEi
EB1730

Phylogenomic databases

eggNOGiCOG0691, Bacteria
HOGENOMiCLU_108953_3_0_6
InParanoidiP0A832
KOiK03664
PhylomeDBiP0A832

Enzyme and pathway databases

BioCyciEcoCyc:EG11782-MONOMER
ECOL316407:JW2601-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P0A832

Family and domain databases

CDDicd09294, SmpB, 1 hit
Gene3Di2.40.280.10, 1 hit
HAMAPiMF_00023, SmpB, 1 hit
InterProiView protein in InterPro
IPR023620, SmpB
IPR000037, SsrA-bd_prot
IPR020081, SsrA-bd_prot_CS
PANTHERiPTHR30308, PTHR30308, 1 hit
PfamiView protein in Pfam
PF01668, SmpB, 1 hit
SUPFAMiSSF74982, SSF74982, 1 hit
TIGRFAMsiTIGR00086, smpB, 1 hit
PROSITEiView protein in PROSITE
PS01317, SSRP, 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 nameiSSRP_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: P0A832
Secondary accession number(s): P32052, P77011
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: August 12, 2020
This is version 109 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, 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
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