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Protein

GDP-mannose 3,5-epimerase 1

Gene

GME-1

Organism
Oryza sativa subsp. japonica (Rice)
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

Catalyzes a reversible epimerization of GDP-D-mannose that precedes the committed step in the biosynthesis of vitamin C (L-ascorbate), resulting in the hydrolysis of the highly energetic glycosyl-pyrophosphoryl linkage. Able to catalyze 2 distinct epimerization reactions and can release both GDP-L-galactose and GDP-L-gulose from GDP-mannose.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

NAD+Curated

<p>This subsection of the ‘Function’ section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Strongly activated by NAD. Activated by NADP. Slightly activated by NADH and NADPH. Inhibited by GDP.1 Publication

<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

The catalytic efficiency increases by 2-fold in the presence of NAD+.
  1. KM=7.12 µM for GDP-mannose1 Publication
  2. KM=12 µM for GDP-mannose (in the presence of 20 µM NAD+)1 Publication

    pH dependencei

    Optimum pH is 7.5-8.0 at 20 degrees Celsius, and 8.0-8.5 at 25 degrees Celsius in the presence of NAD+.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway

    This protein is involved in step 1 of the subpathway that synthesizes L-ascorbate from GDP-alpha-D-mannose.1 Publication
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. GDP-mannose 3,5-epimerase 1 (GME-1), GDP-mannose 3,5-epimerase 2 (GME-2)
    2. no protein annotated in this organism
    3. no protein annotated in this organism
    4. no protein annotated in this organism
    5. no protein annotated in this organism
    This subpathway is part of the pathway L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-ascorbate from GDP-alpha-D-mannose, the pathway L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 sitei60NADBy similarity1
    Binding sitei80NADBy similarity1
    Binding sitei105Substrate; via carbonyl oxygenBy similarity1
    <p>This subsection of the ‘Function’ 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 sitei175Proton acceptorBy similarity1
    Binding sitei175NADBy similarity1
    Binding sitei179NADBy similarity1
    Binding sitei204SubstrateBy similarity1
    Binding sitei226SubstrateBy similarity1
    Binding sitei307SubstrateBy similarity1
    Binding sitei357SubstrateBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi36 – 62NADBy similarityAdd BLAST27

    <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 functionIsomerase
    Biological processAscorbate biosynthesis
    LigandNAD

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-11941

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    5.1.3.18 4460

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    A3C4S4

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00990;UER00931

    <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:
    GDP-mannose 3,5-epimerase 1 (EC:5.1.3.18)
    Short name:
    GDP-Man 3,5-epimerase 1
    Alternative name(s):
    OsGME-1
    <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:GME-1
    Ordered Locus Names:Os10g0417600, LOC_Os10g28200
    ORF Names:OsJ_030296, OSJNBa0061K21.15
    <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>OrganismiOryza sativa subsp. japonica (Rice)
    <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 identifieri39947 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
    <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
    • UP000059680 <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 10

    <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_00002336971 – 378GDP-mannose 3,5-epimerase 1Add BLAST378

    Proteomic databases

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

    More...
    PaxDbi
    A3C4S4

    PTM databases

    iPTMnet integrated resource for PTMs in systems biology context

    More...
    iPTMneti
    A3C4S4

    <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

    Gene expression databases

    ExpressionAtlas, Differential and Baseline Expression

    More...
    ExpressionAtlasi
    A3C4S4 differential

    Genevisible search portal to normalized and curated expression data from Genevestigator

    More...
    Genevisiblei
    A3C4S4 OS

    <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

    Homodimer.By similarity

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    39947.LOC_Os10g28200.1

    <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

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    A3C4S4

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

    More...
    SMRi
    A3C4S4

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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>Regioni145 – 147Substrate bindingBy similarity3
    Regioni217 – 219Substrate bindingBy similarity3
    Regioni242 – 244Substrate bindingBy similarity3

    <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

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    KOG1429 Eukaryota
    COG0451 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000168017

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    A3C4S4

    KEGG Orthology (KO)

    More...
    KOi
    K10046

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    GPMPHNG

    Database of Orthologous Groups

    More...
    OrthoDBi
    EOG09360B69

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd05273 GME-like_SDR_e, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001509 Epimerase_deHydtase
    IPR033890 GDP-Man_epi
    IPR036291 NAD(P)-bd_dom_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01370 Epimerase, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51735 SSF51735, 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>.<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.

    A3C4S4-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MGSSEKNGTA YGEYTYAELE REQYWPSEKL RISITGAGGF IGSHIARRLK
    60 70 80 90 100
    SEGHYIIASD WKKNEHMTED MFCHEFHLVD LRVMDNCLKV TNGVDHVFNL
    110 120 130 140 150
    AADMGGMGFI QSNHSVIMYN NTMISFNMLE AARINGVKRF FYASSACIYP
    160 170 180 190 200
    EFKQLETNVS LKESDAWPAE PQDAYGLEKL ATEELCKHYT KDFGIECRVG
    210 220 230 240 250
    RFHNIYGPFG TWKGGREKAP AAFCRKAQTS TDRFEMWGDG LQTRSFTFID
    260 270 280 290 300
    ECVEGVLRLT KSDFREPVNI GSDEMVSMNE MAEIILSFED RELPIHHIPG
    310 320 330 340 350
    PEGVRGRNSD NTLIKEKLGW APTMKLKDGL RFTYFWIKEQ IEKEKTQGVD
    360 370
    IAGYGSSKVV STQAPVQLGS LRAADGKE
    Length:378
    Mass (Da):42,778
    Last modified:March 20, 2007 - 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:i4BAE83BB932C321A
    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 ABG66078 differs from that shown. Reason: Erroneous gene model prediction.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
    AB193582 mRNA Translation: BAD66930.1
    AC016780 Genomic DNA Translation: AAM08784.1
    DP000086 Genomic DNA Translation: ABB47619.2
    DP000086 Genomic DNA Translation: ABG66078.1 Sequence problems.
    AP008216 Genomic DNA Translation: BAF26523.1
    AP014966 Genomic DNA Translation: BAT10866.1
    CM000147 Genomic DNA Translation: EAZ16087.1
    AK104822 mRNA Translation: BAG96977.1

    NCBI Reference Sequences

    More...
    RefSeqi
    XP_015614669.1, XM_015759183.1

    UniGene gene-oriented nucleotide sequence clusters

    More...
    UniGenei
    Os.8361

    Genome annotation databases

    Ensembl plant genome annotation project

    More...
    EnsemblPlantsi
    Os10t0417600-01; Os10t0417600-01; Os10g0417600

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    4348636

    Gramene; a comparative resource for plants

    More...
    Gramenei
    Os10t0417600-01; Os10t0417600-01; Os10g0417600

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    osa:4348636

    <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
    AB193582 mRNA Translation: BAD66930.1
    AC016780 Genomic DNA Translation: AAM08784.1
    DP000086 Genomic DNA Translation: ABB47619.2
    DP000086 Genomic DNA Translation: ABG66078.1 Sequence problems.
    AP008216 Genomic DNA Translation: BAF26523.1
    AP014966 Genomic DNA Translation: BAT10866.1
    CM000147 Genomic DNA Translation: EAZ16087.1
    AK104822 mRNA Translation: BAG96977.1
    RefSeqiXP_015614669.1, XM_015759183.1
    UniGeneiOs.8361

    3D structure databases

    ProteinModelPortaliA3C4S4
    SMRiA3C4S4
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi39947.LOC_Os10g28200.1

    PTM databases

    iPTMnetiA3C4S4

    Proteomic databases

    PaxDbiA3C4S4

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiOs10t0417600-01; Os10t0417600-01; Os10g0417600
    GeneIDi4348636
    GrameneiOs10t0417600-01; Os10t0417600-01; Os10g0417600
    KEGGiosa:4348636

    Phylogenomic databases

    eggNOGiKOG1429 Eukaryota
    COG0451 LUCA
    HOGENOMiHOG000168017
    InParanoidiA3C4S4
    KOiK10046
    OMAiGPMPHNG
    OrthoDBiEOG09360B69

    Enzyme and pathway databases

    UniPathwayi
    UPA00990;UER00931

    BioCyciMetaCyc:MONOMER-11941
    BRENDAi5.1.3.18 4460
    SABIO-RKiA3C4S4

    Gene expression databases

    ExpressionAtlasiA3C4S4 differential
    GenevisibleiA3C4S4 OS

    Family and domain databases

    CDDicd05273 GME-like_SDR_e, 1 hit
    InterProiView protein in InterPro
    IPR001509 Epimerase_deHydtase
    IPR033890 GDP-Man_epi
    IPR036291 NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF01370 Epimerase, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 nameiGME1_ORYSJ
    <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: A3C4S4
    Secondary accession number(s): B7EX80
    , Q0IXP2, Q0R4F5, Q109P5, Q338B5, Q5W7P1, Q8S862
    <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: July 10, 2007
    Last sequence update: March 20, 2007
    Last modified: December 5, 2018
    This is version 84 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 programPlant 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
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