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Entry version 110 (12 Aug 2020)
Sequence version 1 (01 Jun 2003)
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Protein

Alpha-L-rhamnosidase

Gene

SAVERM_828

Organism
Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)
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

Alpha-L-rhamnosidase which is able to degrade p-nitrophenyl-alpha-L-rhamnopyranoside (PNP-Rha) in vitro. Releases L-rhamnose from citrus flavonoids such as naringin, rutin and hesperidin, and the arabinogalactan-protein (AGP) gum arabic. AGPs are a family of proteoglycans that are localized on the cell surfaces of higher plants. Cleaves both the alpha-1,6 and the alpha-1,2-linked rhamnosyl residues.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 1.93 sec(-1) with p-nitrophenyl-alpha-L-rhamnopyranoside as substrate.1 Publication
  1. KM=0.03 mM for p-nitrophenyl-alpha-L-rhamnopyranoside1 Publication

    pH dependencei

    Optimum pH is 6.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi179CalciumCombined sources1
    Metal bindingi180CalciumCombined sources1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei203L-rhamnose 2Combined sources1
    Metal bindingi228CalciumCombined sources1
    Metal bindingi233Calcium; via carbonyl oxygenCombined sources1
    Binding sitei630L-rhamnose 1Combined sources1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei636Proton donor1 Publication1
    Binding sitei643L-rhamnose 1Combined sources1
    Binding sitei695L-rhamnose 1Combined sources1
    Active sitei895Proton acceptor1 Publication1
    Binding sitei916L-rhamnose 1Combined sources1

    <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

    <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 functionHydrolase
    LigandCalcium, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-20550

    <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:
    Alpha-L-rhamnosidase1 Publication (EC:3.2.1.401 Publication)
    Alternative name(s):
    Rha78A1 Publication
    <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
    ORF Names:SAVERM_828
    <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>OrganismiStreptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)
    <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 identifieri227882 [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 lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces
    <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
    • UP000000428 <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

    <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

    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>Mutagenesisi179D → A: Abrogates L-rhamnose binding. 1 Publication1
    Mutagenesisi180N → A: Abrogates L-rhamnose binding. 1 Publication1
    Mutagenesisi636E → D or Q: Drastically reduces alpha-L-rhamnosidase activity. 1 Publication1
    Mutagenesisi895E → D or Q: Drastically reduces alpha-L-rhamnosidase activity. 1 Publication1

    <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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004483131 – 1030Alpha-L-rhamnosidaseAdd BLAST1030

    <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

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    227882.SAV_828

    <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

    11030
    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
    Q82PP4

    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

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni133 – 297Carbohydrate-binding module-67 (CBM67)1 PublicationAdd BLAST165
    Regioni179 – 180L-rhamnose 2 bindingCombined sources2
    Regioni634 – 636L-rhamnose 1 bindingCombined sources3

    <p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

    The carbohydrate-binding module-67 (CBM67) binds L-rhamnose, it does not bind L-galactose or L-fucose, demonstrating that stereochemistry of the sugar at C4 and/or C2 are important specificity determinants. Also, removal of calcium through chelation or mutation abrogates L-rhamnose binding, confirming the importance of calcium in the binding of its ligand.1 Publication

    <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 glycosyl hydrolase 78 family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG3250, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_002926_3_0_11

    KEGG Orthology (KO)

    More...
    KOi
    K05989

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    IWERLNS

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.50.10.10, 1 hit
    2.60.120.260, 1 hit
    2.60.40.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR008928, 6-hairpin_glycosidase_sf
    IPR012341, 6hp_glycosidase-like_sf
    IPR016007, Alpha_rhamnosid
    IPR035396, Bac_rhamnosid6H
    IPR035398, Bac_rhamnosid_C
    IPR013737, Bac_rhamnosid_N
    IPR036116, FN3_sf
    IPR008979, Galactose-bd-like_sf
    IPR013783, Ig-like_fold
    IPR008902, Rhamnosid_concanavalin

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF05592, Bac_rhamnosid, 1 hit
    PF17389, Bac_rhamnosid6H, 1 hit
    PF17390, Bac_rhamnosid_C, 1 hit
    PF08531, Bac_rhamnosid_N, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF010631, A-rhamnsds, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF48208, SSF48208, 1 hit
    SSF49265, SSF49265, 1 hit
    SSF49785, SSF49785, 2 hits

    <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.

    Q82PP4-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSALRVTSPS VEYVQRPLGL DAAHPRLSWP MASAAPGRRQ SAYQVRVASS
    60 70 80 90 100
    AAGLSHPDVW DSGKVVSDDS VLVPYAGPPL KPRTRYFWSV RVWDADGGAS
    110 120 130 140 150
    EWSAPSWWET GLMGASQWSA KWISAPAPLT EAPSLEGSSW IWFPEGEPAN
    160 170 180 190 200
    SAPAATRWFR RTVDLPDDIT GATLAISADN VYAVSVDGAE VARTDLEADN
    210 220 230 240 250
    EGWRRPAVID VLDHVHSGNN TLAVSASNAS VGPAGWICVL VLTTASGEKK
    260 270 280 290 300
    IFSDASWKST DHEPADGWRE PDFDDSGWPA AKVAAAWGAG PWGRVAPVAS
    310 320 330 340 350
    AANQLRHEFR LPHKKVSRAR LYATALGLYE AHLNGRRVGR DQLAPGWTDY
    360 370 380 390 400
    RKRVQYQTYD VTSSVRPGAN ALAAYVAPGW YAGNVGMFGP HQYGERPALL
    410 420 430 440 450
    AQLEVEYADG TSERITSGPD WRAASGPIVS ADLLSGETYD ARKETAGWTS
    460 470 480 490 500
    PGFDDRAWLA VRGADNDVPE QIVAQVDGPV RIAKELPARK VTEPKPGVFV
    510 520 530 540 550
    LDLGQNMVGS VRLRVSGDAG TTVRLRHAEV LNPDGTIYTA NLRSAAATDT
    560 570 580 590 600
    YTLKGQGEET YEPRFTFHGF RYVEVTGFPG KPSTTSVTGR VMHTSAPFTF
    610 620 630 640 650
    EFETNVPMLN KLHSNITWGQ RGNFLSVPTD TPARDERLGW TGDINVFAPT
    660 670 680 690 700
    AAYTMESARF LTKWLVDLRD AQTSDGAFTD VAPAVGNLGN GVAGWGDAGV
    710 720 730 740 750
    TVPWALYQAY GDRQVLADAL PSVHAWLRYL EKHSDGLLRP ADGYGDWLNV
    760 770 780 790 800
    SDETPKDVIA TAYFAHSADL AARMATELGK DAAPYTDLFT RIRKAFQTAY
    810 820 830 840 850
    VASDGKVKGD TQSAYVLTLS MNLVPDALRK AAADRLVALI EAKDWHLSTG
    860 870 880 890 900
    FLGTPRLLPV LTDTGHTDVA YRLLHQRTFP SWGYPIDKGS TTMWERWDSI
    910 920 930 940 950
    QPDGGFQTPE MNSFNHYAYG SVGEWMYANI AGIAPGRAGY RQVVIRPRPG
    960 970 980 990 1000
    GEVTSARATF ASLHGPVSTR WQQRSGGFVL TCSVPPNTTA EVWIPADHPD
    1010 1020 1030
    RVQHTHGTFV RAEDGCAVFE VGSGSHRFTV
    Length:1,030
    Mass (Da):111,886
    Last modified:June 1, 2003 - 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:i7E9D6E2852C27764
    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
    BA000030 Genomic DNA Translation: BAC68538.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    BAC68538; BAC68538; SAVERM_828

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    sma:SAVERM_828

    <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
    BA000030 Genomic DNA Translation: BAC68538.1

    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
    3W5MX-ray1.80A1-1030[»]
    3W5NX-ray1.80A1-1030[»]
    SMRiQ82PP4
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi227882.SAV_828

    Genome annotation databases

    EnsemblBacteriaiBAC68538; BAC68538; SAVERM_828
    KEGGisma:SAVERM_828

    Phylogenomic databases

    eggNOGiCOG3250, Bacteria
    HOGENOMiCLU_002926_3_0_11
    KOiK05989
    OMAiIWERLNS

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-20550

    Family and domain databases

    Gene3Di1.50.10.10, 1 hit
    2.60.120.260, 1 hit
    2.60.40.10, 1 hit
    InterProiView protein in InterPro
    IPR008928, 6-hairpin_glycosidase_sf
    IPR012341, 6hp_glycosidase-like_sf
    IPR016007, Alpha_rhamnosid
    IPR035396, Bac_rhamnosid6H
    IPR035398, Bac_rhamnosid_C
    IPR013737, Bac_rhamnosid_N
    IPR036116, FN3_sf
    IPR008979, Galactose-bd-like_sf
    IPR013783, Ig-like_fold
    IPR008902, Rhamnosid_concanavalin
    PfamiView protein in Pfam
    PF05592, Bac_rhamnosid, 1 hit
    PF17389, Bac_rhamnosid6H, 1 hit
    PF17390, Bac_rhamnosid_C, 1 hit
    PF08531, Bac_rhamnosid_N, 1 hit
    PIRSFiPIRSF010631, A-rhamnsds, 1 hit
    SUPFAMiSSF48208, SSF48208, 1 hit
    SSF49265, SSF49265, 1 hit
    SSF49785, SSF49785, 2 hits

    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 nameiRHA78_STRAW
    <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: Q82PP4
    <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: October 16, 2019
    Last sequence update: June 1, 2003
    Last modified: August 12, 2020
    This is version 110 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, 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. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
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