cho:Gene Product(s): Difference between revisions
deleting ModBase and PDB from accessions table on gp pages |
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****************************************************************************************** -->{{Product_nomenclature_help}} | ****************************************************************************************** -->{{Product_nomenclature_help}} | ||
{| | {| id="L46aa7b3bd94bc" class=" tableEdit Product_nomenclature_table" | ||
|- | |- | ||
!align=left {{table heading style}} |Standard name | !align=left {{table heading style}} |Standard name | ||
|| | || | ||
Cho | |||
|- | |- | ||
!align=left {{table heading style}} |Synonyms | !align=left {{table heading style}} |Synonyms | ||
|| | || | ||
endonuclease of nucleotide excision repair<ref name='LIB:Riley_2006'/>, YdjQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cho<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1741<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> | ''endonuclease of nucleotide excision repair<ref name='LIB:Riley_2006'/>, YdjQ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cho<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1741<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , dinM, ECK1739, JW1730, sosD, ydjQ, b1741'' | ||
|- | |- | ||
!align=left {{table heading style}} |Product description | !align=left {{table heading style}} |Product description | ||
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.- 3.1.25.-]<ref name='LIB:Riley_2006'/> | * [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.- 3.1.25.-]<ref name='LIB:Riley_2006'/> | ||
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****************************************************************************************** -->{{Product_GO_help}} | ****************************************************************************************** -->{{Product_GO_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46aa7b3cf0ab3" class=" tableEdit GO_table_product dataTable" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Qualifier!!GO ID!!GO term name!!Reference | !|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status | ||
|- | |- | ||
| | | | ||
| | | | ||
GO: | GO:0005737 | ||
| | |||
cytoplasm | |||
| | |||
| | |||
| | |||
| | |||
C | |||
| | |||
Seeded from Riley et al 2006 <ref name='LIB:Riley_2006'/>. | |||
| | |||
Missing: evidence, reference | |||
|- | |||
| | |||
| | |||
GO:0004518 | |||
| | | | ||
nuclease activity | |||
| | | | ||
GO_REF: | GOA:interpro<br />GO_REF:0000002 | ||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| | | | ||
InterPro:IPR000305 | |||
| | | | ||
F | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
| Line 101: | Line 120: | ||
| | | | ||
GO: | GO:0004518 | ||
| | | | ||
nuclease activity | |||
| | | | ||
GOA:spkw<br />SP_KW:GO_REF:0000004 | |||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| | | | ||
SP_KW:KW-0267 | |||
| | | | ||
F | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
| Line 124: | Line 143: | ||
intracellular | intracellular | ||
| | | | ||
GO_REF:0000002 | GOA:interpro<br />GO_REF:0000002 | ||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| Line 132: | Line 151: | ||
C | C | ||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
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| | | | ||
GO: | GO:0006281 | ||
| | | | ||
DNA repair | |||
| | | | ||
GOA:interpro<br />GO_REF:0000002 | |||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| | | | ||
InterPro:IPR000305 | InterPro:IPR000305 | ||
| | | | ||
P | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
| Line 158: | Line 177: | ||
| | | | ||
GO: | GO:0006281 | ||
| | | | ||
DNA repair | |||
| | | | ||
GO_REF:0000004 | GOA:spkw<br />SP_KW:GO_REF:0000004 | ||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| | | | ||
SP_KW:KW- | SP_KW:KW-0228 | ||
| | | | ||
P | P | ||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
| Line 177: | Line 196: | ||
| | | | ||
GO: | GO:0006281 | ||
| | | | ||
DNA repair | |||
| | | | ||
GO_REF:0000004 | GOA:spkw<br />SP_KW:GO_REF:0000004 | ||
| | | | ||
IEA: Inferred from Electronic Annotation | IEA: Inferred from Electronic Annotation | ||
| | | | ||
SP_KW:KW- | SP_KW:KW-0234 | ||
| | | | ||
P | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
| Line 196: | Line 215: | ||
| | | | ||
GO: | GO:0006974 | ||
| | | | ||
response to DNA damage stimulus | |||
| | | | ||
GOA:spkw<br />SP_KW:GO_REF:0000004 | |||
| | | | ||
IEA: Inferred from Electronic Annotation | |||
| | | | ||
SP_KW:KW-0227 | |||
| | | | ||
P | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | complete | ||
|- | |- | ||
| | | | ||
| | | | ||
GO: | GO:0009432 | ||
| | | | ||
SOS response | |||
| | | | ||
GOA:spkw<br />SP_KW:GO_REF:0000004 | |||
| | | | ||
IEA: Inferred from Electronic Annotation | |||
| | | | ||
SP_KW:KW-0742 | |||
| | | | ||
P | |||
| | | | ||
Seeded from | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | |||
|- | |- | ||
| | | | ||
| | | | ||
GO: | GO:0016787 | ||
| | | | ||
hydrolase activity | |||
| | | | ||
GOA:spkw<br />SP_KW:GO_REF:0000004 | |||
| | | | ||
IEA: Inferred from Electronic Annotation | |||
| | | | ||
SP_KW:KW-0378 | |||
| | | | ||
F | |||
| | | | ||
Seeded from EcoCyc | Seeded from [[EcoCyc]] (v14.0) | ||
| | | | ||
complete | |||
|- | |- | ||
| | | | ||
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complete | complete | ||
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****************************************************************************************** -->{{Product_interactions_help}} | ****************************************************************************************** -->{{Product_interactions_help}} | ||
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|- {{table heading style}} | |- {{table heading style}} | ||
!|Partner Type!!Partner!!Notes!!References!!Evidence | !|Partner Type!!Partner!!Notes!!References!!Evidence | ||
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Experiment(s):EBI-1140667<br /> | Experiment(s):EBI-1140667<br /> | ||
|- | |||
| | |||
Protein | |||
| | |||
groL | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
MALDI(Z-score):17.053160 | |||
|- | |||
| | |||
Protein | |||
| | |||
groS | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
MALDI(Z-score):28.255864 | |||
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****************************************************************************************** -->{{Product_localization_help}} | ****************************************************************************************** -->{{Product_localization_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="D46a80c8a77f3c" class=" tableEdit Product_localization_table" | ||
|- {{table heading style}} | |- {{table heading style}} | ||
!|Compartment!!Description!!Evidence!!Notes | !|Compartment!!Description!!Evidence!!Reference/Source!!Notes | ||
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****************************************************************************************** -->{{Product_physical_properties_help}} | ****************************************************************************************** -->{{Product_physical_properties_help}} | ||
{| | {| id="K46aa7b5071fbc" class=" tableEdit Product_phys_prop_table" | ||
|- | |||
!align=left {{table heading style}} |Name | |||
|| | |||
|- | |- | ||
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40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 C residues) | 40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 C residues) | ||
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****************************************************************************************** -->{{Product_domains_motifs_help}} | ****************************************************************************************** -->{{Product_domains_motifs_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46aa7b50f2b4b" class=" tableEdit Product_motif_table dataTable" | ||
|- {{table heading style}} | |- {{table heading style}} | ||
!|Type!!Residues!!Description!!Notes | !|Type!!Residues!!Description!!Notes!!References | ||
|- | |||
| | |||
Domain | |||
| | |||
34..109 | |||
| | |||
[http://pfam.janelia.org/family/PF01541 PF01541 GIY-YIG catalytic domain] | |||
| | |||
| | |||
PMID:19920124 | |||
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****************************************************************************************** -->{{Product_structure_help}} | ****************************************************************************************** -->{{Product_structure_help}} | ||
{| | {| id="B46a80c8c15c4f" class=" tableEdit Product_structure_table" | ||
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|| | || | ||
View models at: | View models at: | ||
* [http:// | * [http://www.proteinmodelportal.org/query/uniprot/P76213 Protein Model Portal] | ||
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76213 PSI-PRED (P76213)] | |||
* [http://bioinf.cs.ucl.ac.uk/ | * [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76213 Genomes TO Protein (P76213)] (GTOP) | ||
* [http://spock.genes.nig.ac.jp/~genome/ | |||
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****************************************************************************************** -->{{Product_resources_help}} | ****************************************************************************************** -->{{Product_resources_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z46aa7b51c4c04" class=" tableEdit Product_resource_table" | ||
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!|Resource type!!Source!!Notes/Reference | !|Resource type!!Source!!Notes/Reference | ||
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****************************************************************************************** -->{{Gene_accessions_help}} | ****************************************************************************************** -->{{Gene_accessions_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R46aa7b5231af9" class=" tableEdit Gene_accessions_table" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
|- | |- | ||
| | | | ||
[http:// | [http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]]) | ||
| | |||
[http://www.ncbi.nlm.nih.gov/protein/16129695 GI:16129695] | |||
| | |||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]]) | |||
| | |||
[http://www.ncbi.nlm.nih.gov/protein/NP_416255.1 GeneID:948996] | |||
| | |||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[[ASAP]] | |||
| | |||
ASAP:ABE-0005807 | |||
| | |||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |||
| | |||
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]]) | |||
| | |||
[http://www.uniprot.org/uniprot/P76213 UniProtKB/Swiss-Prot:P76213] | |||
| | |||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[[EcoCyc]] | |||
| | |||
EcoCyc:G6937 | |||
| | |||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |||
| | |||
[[EcoGene]] | |||
| | | | ||
EcoGene:EG13993 | |||
| | | | ||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |- | ||
| | | | ||
[http:// | [http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]]) | ||
| | | | ||
[ | [http://www.ncbi.nlm.nih.gov/gene?term=948996 GeneID:948996] | ||
| | | | ||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |- | ||
| | | | ||
[[RegulonDB]] | |||
| | | | ||
RegulonDB:ECK120003525 | |||
| | | | ||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |- | ||
| | | | ||
[[EchoBASE]] | |||
| | | | ||
EchoBASE:EB3749 | |||
| | | | ||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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Latest revision as of 20:42, 17 February 2015
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| 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 |
Cho |
|---|---|
| Synonyms |
endonuclease of nucleotide excision repair[1], YdjQ[2][1], Cho[2][1], B1741[2][1] , dinM, ECK1739, JW1730, sosD, ydjQ, b1741 |
| Product description |
endonuclease of nucleotide excision repair[2][3] Endonuclease involved in excision repair, cuts 3' of lesion; requires UvrAB[4] |
| EC number (for enzymes) | |
| edit table |
Notes
Function
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:0004518 |
nuclease activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004518 |
nuclease activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005622 |
intracellular |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006281 |
DNA repair |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006281 |
DNA repair |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006281 |
DNA repair |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006974 |
response to DNA damage stimulus |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0009432 |
SOS response |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0016787 |
hydrolase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006974 |
response to DNA damage stimulus |
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 |
groL |
Experiment(s):EBI-883032 | ||
|
Protein |
rplQ |
Experiment(s):EBI-1140667 | ||
|
Protein |
dnaK |
Experiment(s):EBI-1140667 | ||
|
Protein |
rpsI |
Experiment(s):EBI-1140667 | ||
|
Protein |
groL |
Experiment(s):EBI-1140667 | ||
|
Protein |
uspG |
Experiment(s):EBI-1140667 | ||
|
Protein |
groL |
MALDI(Z-score):17.053160 | ||
|
Protein |
groS |
MALDI(Z-score):28.255864 | ||
| 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
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MVRRLTSPRL EFEAAAIYEY PEHLRSFLND LPTRPGVYLF HGESDTMPLY IGKSVNIRSR VLSHLRTPDE AAMLRQSRRI SWICTAGEIG ALLLEARLIK EQQPLFNKRL RRNRQLCALQ LNEKRVDVVY AKEVDFSRAP NLFGLFANRR AALQALQTIA DEQKLCYGLL GLEPLSRGRA CFRSALKRCA GACCGKESHE EHALRLRQSL ERLRVVCWPW QGAVALKEQH PEMTQYHIIQ NWLWLGAVNS LEEATTLIRT PAGFDHDGYK ILCKPLLSGN YEITELDPAN DQRAS |
| Length |
295 |
| Mol. Wt |
33.739 kDa |
| pI |
9.0 (calculated) |
| Extinction coefficient |
40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
|
Structure figures
Notes
Gene Product Resources
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
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ Fernández De Henestrosa, AR et al. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35 1560-72 PubMed
- ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 7.0 7.1 7.2 7.3 7.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
- ↑ 8.0 8.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
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