add:Gene Product(s): Difference between revisions

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Updating UniProt accessions on gene product page in accessions table.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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adenosine deaminase<ref name='LIB:Riley_2006'/>, B1623<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Add<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''adenosine deaminase<ref name='LIB:Riley_2006'/>, B1623<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Add<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1618, JW1615, b1623''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
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Missing: evidence  
Missing: evidence, reference
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adenosine deaminase activity
adenosine deaminase activity
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PMID:765747  
PMID:765747
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IMP: Inferred from Mutant Phenotype
IMP: Inferred from Mutant Phenotype
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binding
binding
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PMID:3486673  
PMID:3486673
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ISS: Inferred from Sequence or Structural Similarity
ISS: Inferred from Sequence or Structural Similarity
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complete
Missing: with/from
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response to DNA damage stimulus
response to DNA damage stimulus
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PMID:11967071  
PMID:11967071
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IEP: Inferred from Expression Pattern
IEP: Inferred from Expression Pattern
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa72eb9d42b"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P22333 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P22333 PSI-PRED (P22333)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P22333 Genomes TO Protein (P22333)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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{|   id="C46aa72ecb0698"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aa72ecb0698"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/16129581 GI:16129581]
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Escherichia coli str. K-12 substr. MG1655
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=ADENODEAMIN-MONOMER EcoCyc:ADENODEAMIN-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/NP_416140.1 GeneID:945851]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0005435
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P22333 UniProtKB/Swiss-Prot:P22333]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG10030
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10030
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P22333 UniProt:P22333]
[http://www.ncbi.nlm.nih.gov/gene?term=945851 GeneID:945851]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.janelia.org/protein/P22333 Pfam:P22333]
RegulonDB:ECK120000027
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416140 RefSeq:NP_416140]
EchoBASE:EB0029
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:40, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Add

Synonyms

adenosine deaminase[1], B1623[2][1], Add[2][1] , ECK1618, JW1615, b1623

Product description

Adenosine deaminase; mutants affect growth on deoxyadenosine in purA, B mutants[3]

EC number (for enzymes)
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Notes

Adenosine deaminase is the enzyme that catalyzes the irreversible deamination of adenosine or deoxyadenosine to inosine or deoxyinosine. The active site of ADA contains residues of a Histidine, 2 Aspartic acids, one Glutamic acid, and a zinc atom. The overall mechanism involves a hydroxyl group addition to C6 of adenosine, which forms the tetrahedral transition state intermediate. Then, the ammonia elimination forms inosine. Zinc acts as a powerful electrophile, which allows a water molecule to attack C6. Glutamic acid interacts with N1 and donates a proton, reducing the N1=C6 double bond character, allowing the hydroxyl nucleophilic attack. A Histidine residue and the carboxylic group of aspartic acid stabilizes and orients the zinc-bound water molecule. The ammonia elimination pathway is not quite understood but is the final step in the mechanism of adenosine deaminase.

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004000

adenosine deaminase activity

PMID:4874315[4]

IDA: Inferred from Direct Assay

F

complete

GO:0004000

adenosine deaminase activity

PMID:765747[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0015950

purine nucleotide interconversion

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0004000

adenosine deaminase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00540

F

Seeded from EcoCyc (v14.0)

complete

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0004000

adenosine deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006330

F

Seeded from EcoCyc (v14.0)

complete

GO:0005488

binding

PMID:3486673[7]

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P56658

F

CHEBI:27834 (Deoxycoformycin mechanistically inhibits Add).

complete

GO:0006154

adenosine catabolic process

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0004000

adenosine deaminase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.4.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0004000

adenosine deaminase activity

PMID:5335916[8]

IDA: Inferred from Direct Assay

F

complete

GO:0032261

purine nucleotide salvage

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0006154

adenosine catabolic process

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0043103

hypoxanthine salvage

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0009117

nucleotide metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0546

P

Seeded from EcoCyc (v14.0)

complete

GO:0046101

hypoxanthine biosynthetic process

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

EcoliWiki:guaA


P

complete

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00540

P

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:5335916[8]

IC: Inferred by Curator

C

Missing: with/from

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001365

P

Seeded from EcoCyc (v14.0)

complete

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006330

P

Seeded from EcoCyc (v14.0)

complete

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006650

P

Seeded from EcoCyc (v14.0)

complete

GO:0009168

purine ribonucleoside monophosphate biosynthetic process

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0015950

purine nucleotide interconversion

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0032261

purine nucleotide salvage

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0043103

hypoxanthine salvage

PMID:1998686[6]

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006974

response to DNA damage stimulus

PMID:11967071[9]

IEP: Inferred from Expression Pattern

P

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

rpsM

PMID:16606699[10]

Experiment(s):EBI-1140315

Protein

arpA

PMID:16606699[10]

Experiment(s):EBI-1140315

Protein

rplT

PMID:16606699[10]

Experiment(s):EBI-1140315

Protein

insC1

PMID:16606699[10]

Experiment(s):EBI-1140315

Protein

ligA

PMID:16606699[10]

Experiment(s):EBI-1140315

Protein

gcd

PMID:16606699[10]

Experiment(s):EBI-1140315

Small Molecule

CHEBI:27834 (Deoxycoformycin)

Inhibitor of Add activity


edit table


Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table


Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MIDTTLPLTD IHRHLDGNIR PQTILELGRQ YNISLPAQSL ETLIPHVQVI ANEPDLVSFL
TKLDWGVKVL ASLDACRRVA FENIEDAARH GLHYVELRFS PGYMAMAHQL PVAGVVEAVI
DGVREGCRTF GVQAKLIGIM SRTFGEAACQ QELEAFLAHR DQITALDLAG DELGFPGSLF
LSHFNRARDA GWHITVHAGE AAGPESIWQA IRELGAERIG HGVKAIEDRA LMDFLAEQQI
GIESCLTSNI QTSTVAELAA HPLKTFLEHG IRASINTDDP GVQGVDIIHE YTVAAPAAGL
SREQIRQAQI NGLEMAFLSA EEKRALREKV AAK
Length

333

Mol. Wt

36.397 kDa

pI

5.4 (calculated)

Extinction coefficient

22,460 - 22,960 (calc based on 4 Y, 3 W, and 4 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

5..329

PF00962 Adenosine/AMP deaminase

PMID:19920124[11]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=add taxon=562,83333 </beststructure>

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129581

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945851

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005435

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P22333

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10030

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10030

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945851

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000027

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0029

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

[back to top]




References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ Remy, CN & Love, SH (1968) Induction of adenosine deaminase in Escherichia coli. J. Bacteriol. 96 76-85 PubMed
  5. ↑ Jochimsen, B et al. (1975) Location on the chromosome of Escherichia coli of genes governing purine metabolism. Adenosine deaminase (add), guanosine kinase (gsk) and hypoxanthine phosphoribosyltransferase (hpt). Mol. Gen. Genet. 143 85-91 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 Chang, ZY et al. (1991) Deduced amino acid sequence of Escherichia coli adenosine deaminase reveals evolutionarily conserved amino acid residues: implications for catalytic function. Biochemistry 30 2273-80 PubMed
  7. ↑ Frick, L et al. (1986) Transition-state stabilization by adenosine deaminase: structural studies of its inhibitory complex with deoxycoformycin. Biochemistry 25 1616-21 PubMed
  8. ↑ 8.0 8.1 Wolfenden, R et al. (1967) Substrate binding by adenosine deaminase. Specificity, pH dependence, and competition by mercurials. J. Biol. Chem. 242 977-83 PubMed
  9. ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
  10. ↑ 10.0 10.1 10.2 10.3 10.4 10.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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