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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	vsr
Gene Synonym(s)	ECK1958, b1960, JW1943^[1], JW1943
Product Desc.	DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway^[2]^[3] Mismatch nicking endonuclease, helps repair TG mismatches^[4]
Product Synonyms(s)	DNA mismatch endonuclease of very short patch repair^[1], B1960^[2]^[1], Vsr^[2]^[1] , ECK1958, JW1943, b1960
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dcm-vsr^[2]
Regulation/Activity
Quick Links
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Notes

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Mismatch repair minimizes the effects of C methylation.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	vsr
Mnemonic	Very short (patch) repair
Synonyms	ECK1958, b1960, JW1943^[1], JW1943
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	43.72 minutes	MG1655: 2028942..2028472 <gbrowseImage> name=NC_000913:2028472..2028942 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1920955..1921425 <gbrowseImage> name=NC_012759:1920955..1921425 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2033055..2032585 <gbrowseImage> name=NC_007779:2032585..2033055 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2119950..2119480 <gbrowseImage> name=NC_010473:2119480..2119950 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	2028475	Edman degradation	PMID:10360178
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
Δvsr (Keio:JW1943)	deletion	deletion	PMID:16738554	Shigen CGSC9616^[5]
vsr::Tn5KAN-2 (FB20552)	Insertion at nt 394 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20552	does not contain pKD46
vsr::Tn5KAN-2 (FB20553)	Insertion at nt 394 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20553	contains pKD46
Δvsr-734::kan			PMID:16738554	CGSC:103364
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1943	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCGACGTTCACGATAAGGC Primer 2:CCAGCGAGTAAATGAATCCCCTG
25D8	Kohara Phage	Genobase	PMID:3038334
uvrC279::Tn10	Linked marker	CAG12156 = CGSC7394^[5]	est. P1 cotransduction: 21% ^[6]
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[5]	est. P1 cotransduction: 75% ^[6]
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Notes

Accessions in Other Databases

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11068	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11068	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001057	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946476	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1061	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006507	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	Vsr
Synonyms	DNA mismatch endonuclease of very short patch repair^[1], B1960^[2]^[1], Vsr^[2]^[1] , ECK1958, JW1943, b1960
Product description	DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway^[2]^[3] Mismatch nicking endonuclease, helps repair TG mismatches^[4]
EC number (for enzymes)	3.1.-.-^[1]
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Notes

Function

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<protect> 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:0006308	DNA catabolic process				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011335	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	PMID:10612397	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0006298	mismatch repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004603	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006298	mismatch repair	PMID:1944537	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043765	T/G mismatch-specific endonuclease activity	PMID:1944537	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	yibL	PMID:16606699	Experiment(s):EBI-1141500
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1141500
Protein	rplT	PMID:16606699	Experiment(s):EBI-1141500
Protein	malQ	PMID:16606699	Experiment(s):EBI-1141500
	MutL	PMID:19376855
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Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> 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 MADVHDKATR SKNMRAIATR DTAIEKRLAS LLTGQGLAFR VQDASLPGRP DFVVDEYRCV IFTHGCFWHH HHCYLFKVPA TRTEFWLEKI GKNVERDRRD ISRLQELGWR VLIVWECALR GREKLTDEAL TERLEEWICG EGASAQIDTQ GIHLLA
Length	156
Mol. Wt	18.015 kDa
pI	7.5 (calculated)
Extinction coefficient	30,480 - 31,105 (calc based on 2 Y, 5 W, and 5 C residues)
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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
Initiator Methionine	1	Removed	UniProt:P09184
Domain	2..76	PF03852 DNA mismatch endonuclease Vsr		PMID:19920124
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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129906	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946476	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006507	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P09184	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11068	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11068	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946476	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001057	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1061	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	79	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	39	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	28^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
dcm-vsr
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2028922..2028962 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1960 (EcoliWiki Page)	NCBI GEO profiles for vsr
microarray	GenExpDB:b1960 (EcoliWiki Page)	Summary of data for vsr from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to vsr Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11068	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1061	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1960
EcoGene	EcoGene:EG11068	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001057	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006507	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000012494 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	VSR	From SHIGELLACYC
E. coli O157	VSR	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:52980
Pfam (EcoliWiki Page)	PF03852 DNA mismatch endonuclease Vsr
EcoCyc	EcoCyc:EG11068	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11068	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001057	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1061	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006507	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 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 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

vsr:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to vsr Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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