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UniProtKB - P76318 (YEDK_ECOLI)

Entry version 122 (12 Aug 2020)
Sequence version 2 (11 Oct 2004)
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Protein

Abasic site processing protein YedK

Gene

yedK

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

Sensor of abasic sites in single-stranded DNA (ssDNA) required to preserve genome integrity by promoting error-free repair of abasic sites (PubMed:30554877). Recognizes and binds abasic sites in ssDNA at replication forks and chemically modifies the lesion by forming a covalent cross-link with DNA: forms a stable thiazolidine linkage between a ring-opened abasic site and the alpha-amino and sulfhydryl substituents of its N-terminal catalytic cysteine residue (PubMed:30554877, PubMed:31235915, PubMed:31504793). May act as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity).By similarity3 Publications

Miscellaneous

The thiol group of the catalytic Cys-2 is deprotonated by its alpha-amino group to form a thiolate anion that is poised for catalysis (PubMed:31504793). The abasic site sugar moiety is in equilibrium between its cyclic furanose and open-chain aldehyde forms (PubMed:31504793). The Cys-2 thiolate anion attacks the abasic site C1' position to form a covalent bond (PubMed:31504793). The Cys-2 alpha-amino group proton then transfers to the oxygen which is stabilized by the Asn-75 side chain (PubMed:31504793). The O4' rotates to a new position and interacts with the His-160 side chain (PubMed:31504793). The Cys-2 alpha-amino group then attacks the C1' position and transfers a proton to the hydroxyl group to release a water molecule, meanwhile forming a covalent bond with the C1' atom (PubMed:31504793). Thus, a thiazolidine linkage is formed between the abasic site C1' atom and the Cys-2 amino and thiol groups (PubMed:31504793). The Glu-105 side chain carboxyl stabilizes the thiazolidine linkage via a strong hydrogen bond with its amine group (PubMed:31504793).1 Publication

Caution

Was reported to act as an endonuclease that specifically cleaves 5-hydroxymethylcytosine (5hmC)-containing DNA in vitro (PubMed:29020633). Additional experiments are however required to confirm this activity as this protein is present in many organisms that do not utilize methylcytosine for epigenetic control.1 Publication1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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 sitei2Nucleophile2 Publications1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei105Required for sensing abasic sites1 Publication1
Sitei160Required to stabilize abasic sites1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, Hydrolase, Protease
Biological processDNA damage, SOS response

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11662-MONOMER
ECOL316407:JW1916-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:
Abasic site processing protein YedK (EC:3.4.-.-By similarity)
<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:yedK1 Publication
Synonyms:yedG
Ordered Locus Names:b1931, JW1916
<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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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 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>Mutagenesisi2C → A: Abolished formation of the DNA-protein cross-link. Reduced binding to single-stranded DNA. 2 Publications1
Mutagenesisi2C → S: Abolished formation of the DNA-protein cross-link, possibly via the formation of an oxazolidine ring with DNA that is not as stable as a thiazolidine. 1 Publication1
Mutagenesisi4R → A: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi40P → G: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi67W → A: Abolished binding to single-stranded DNA. 1 Publication1
Mutagenesisi68W → A: Abolished binding to single-stranded DNA. 1 Publication1
Mutagenesisi70K → A: Slightly reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi75N → A: Reduced formation of the DNA-protein cross-link. Reduced binding to single-stranded DNA. 2 Publications1
Mutagenesisi77R → A: Abolished binding to single-stranded DNA. 1 Publication1
Mutagenesisi80T → A: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi84S → A: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi85R → A: Strongly reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi105E → A: Reduced formation of the DNA-protein cross-link. Increased binding to single-stranded DNA and further increased affinity for single-stranded DNA containing an abasic site. 2 Publications1
Mutagenesisi106W → A: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi113K → A: Does not affect binding to single-stranded DNA. 1 Publication1
Mutagenesisi149T → A: Reduced formation of the DNA-protein cross-link. Abolished binding to single-stranded DNA. 1 Publication1
Mutagenesisi160H → A: Reduced formation of the DNA-protein cross-link. Slightly increased binding to single-stranded DNA. 2 Publications1
Mutagenesisi162R → A: Abolished binding to single-stranded DNA. 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 <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 methionineiRemovedBy similarity
<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_00001690942 – 222Abasic site processing protein YedKAdd BLAST221

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2Thiazolidine linkage to a ring-opened DNA abasic site2 Publications1

Keywords - PTMi

Covalent protein-DNA linkage

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P76318

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

More...PaxDbi		P76318

PRoteomics IDEntifications database

More...PRIDEi		P76318

<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

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4261039, 9 interactors

Protein interaction database and analysis system

More...IntActi		P76318, 14 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1931

<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

1222
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		P76318

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P76318

<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 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

Glu-105 is involved in sensing abasic sites in single-stranded DNA (ssDNA) (PubMed:31504793). His-160 stabilizes the abasic sites by forming a hydrogen bond with the O4' hydroxyl group (PubMed:31235915).2 Publications

<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 SOS response-associated peptidase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2135, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_035990_6_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P76318

Database for complete collections of gene phylogenies

More...PhylomeDBi		P76318

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.90.1680.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR003738, SRAP
IPR036590, SRAP-like

The PANTHER Classification System

More...PANTHERi		PTHR13604, PTHR13604, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02586, SRAP, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF143081, SSF143081, 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.

P76318-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MCGRFAQSQT REDYLALLAE DIERDIPYDP EPIGRYNVAP GTKVLLLSER 
        60         70         80         90        100
DEHLHLDPVF WGYAPGWWDK PPLINARVET AATSRMFKPL WQHGRAICFA 
       110        120        130        140        150
DGWFEWKKEG DKKQPFFIYR ADGQPIFMAA IGSTPFERGD EAEGFLIVTA 
       160        170        180        190        200
AADQGLVDIH DRRPLVLSPE AAREWMRQEI SGKEASEIAA SGCVPANQFS 
       210        220 
WHPVSRAVGN VKNQGAELIQ PV
Length:222
Mass (Da):24,979
Last modified:October 11, 2004 - 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:iE203A1EA67119F1C
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
L13279 Genomic DNA No translation available.
U00096 Genomic DNA Translation: AAT48139.1
AP009048 Genomic DNA Translation: BAE76551.1

Protein sequence database of the Protein Information Resource

More...PIRi		H64956

NCBI Reference Sequences

More...RefSeqi		WP_000334583.1, NZ_LN832404.1
YP_025310.1, NC_000913.3

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAT48139; AAT48139; b1931
BAE76551; BAE76551; BAE76551

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946435

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1916
eco:b1931

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.2013

<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
L13279 Genomic DNA No translation available.
U00096 Genomic DNA Translation: AAT48139.1
AP009048 Genomic DNA Translation: BAE76551.1
PIRiH64956
RefSeqiWP_000334583.1, NZ_LN832404.1
YP_025310.1, NC_000913.3

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
2ICUX-ray1.60A/B1-222[»]
6KBSX-ray1.60B2-222[»]
6KBUX-ray2.10A/B2-222[»]
6KBXX-ray1.22B2-222[»]
6KBZX-ray1.65B/D/F/H2-222[»]
6KCQX-ray1.70B1-222[»]
6KIJX-ray1.58B2-222[»]
6NUAX-ray1.64A/B2-222[»]
6NUHX-ray1.59A2-222[»]
SMRiP76318
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4261039, 9 interactors
IntActiP76318, 14 interactors
STRINGi511145.b1931

Proteomic databases

jPOSTiP76318
PaxDbiP76318
PRIDEiP76318

Genome annotation databases

EnsemblBacteriaiAAT48139; AAT48139; b1931
BAE76551; BAE76551; BAE76551
GeneIDi946435
KEGGiecj:JW1916
eco:b1931
PATRICifig|511145.12.peg.2013

Organism-specific databases

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

More...EchoBASEi		EB3063

Phylogenomic databases

eggNOGiCOG2135, Bacteria
HOGENOMiCLU_035990_6_1_6
InParanoidiP76318
PhylomeDBiP76318

Enzyme and pathway databases

BioCyciEcoCyc:EG11662-MONOMER
ECOL316407:JW1916-MONOMER

Miscellaneous databases

EvolutionaryTraceiP76318

Protein Ontology

More...PROi		PR:P76318

Family and domain databases

Gene3Di3.90.1680.10, 1 hit
InterProiView protein in InterPro
IPR003738, SRAP
IPR036590, SRAP-like
PANTHERiPTHR13604, PTHR13604, 1 hit
PfamiView protein in Pfam
PF02586, SRAP, 1 hit
SUPFAMiSSF143081, SSF143081, 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 nameiYEDK_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: P76318
Secondary accession number(s): Q2MB05
<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: November 1, 1997
Last sequence update: October 11, 2004
Last modified: August 12, 2020
This is version 122 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, 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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