parE:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''parE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''parE''
Partition
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3021, b3030, JW2998, nfxD''<ref name='LIB:Riley_2006'/>, nfxD''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16617.R46a9ebeb126f6&page=16617&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3021, b3030, JW2998, nfxD''<ref name='LIB:Riley_2006'/>
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===Notes===
===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="F46a9ebeb927d0"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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68.36 minutes&nbsp;
68.36 minutes&nbsp;
|
|
MG1655: 3173418..3171526<br />{{GBrowseFigureByCoord|3170526|3174418|ecoli|MG1655}}
MG1655: 3173418..3171526<br /><gbrowseImage>
name=NC_000913:3171526..3173418
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10687 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10687 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3170526..3174418 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3170526|3174418|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3171526..3173418&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3171526|3173418|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10687 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10687 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3109568..3107676<br /><gbrowseImage>
name=NC_012967:3107676..3109568
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3107676|3109568|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3107676|3109568|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3058674..3060566<br /><gbrowseImage>
name=NC_012759:3058674..3060566
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3058674|3060566|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3058674|3060566|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3174052..3172160<br />{{GBrowseFigureByCoord|3171160|3175052|ecoli_W3110|W3110}}  
W3110: 3174052..3172160<br /><gbrowseImage>
name=NC_007779:3172160..3174052
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3171160|3175052|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3172160|3174052|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3171160..3175052 GBrowse(W3110)]
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3172160..3174052&plugin_action=Go FASTA Dump]
DH10B: 3271163..3269271<br /><gbrowseImage>
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3265487|3274947|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3265487|3274947|FASTA Dump}}
 
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===Notes===
===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="C46a9ebec4fe18"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====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="G46a9ebec9748d"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
|
parEL445H
|
 
|
L445H
|
|
&Delta;parE (Keio:)
 
|
|
deletion
(in strain: DH161; quinolone- resistant)
|
|
deletion
 
|
|


|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P20083 UniProt:P20083]
|-
|
''parEC316Y''
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] 
C316Y
|
|
Sensitivity to
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temperature sensitivity
|
PMID:12509418
|
 
|
identical to wt TopoIV in the superhelical DNA relaxation assay at permissive temperature
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2998
JW2998
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCAACCTCAATCTCCGCCATGTC  
Primer 2:CCAACCTCAATCTCCGCCATGTC  
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[[:Category:Kohara_Phage:17B2|17B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=506 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6B12|6B12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=507 Genobase]
|
PMID:3038334
|-
|
[[metC:Gene|metC162::Tn10]]
|
Linked marker
|
CAG18475 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38931 CGSC7435]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[tolC:Gene|tolC210::Tn10]]
|
Linked marker
|
CAG12184 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38758 CGSC7437]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 80% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
plex5BA-parEC
|
Plasmid Clone
|
 
|
*IPTG-inducible Topo IV expression plasmid
*PMID:10660569
 
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
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|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10687 EcoCyc:EG10687] 
EcoCyc:EG10687
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|-  
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0681 EchoBASE:EB0681] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3030 EcoliGenExpDB:b3030] 
EcoGene:EG10687
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3776 ECOL199310CYC:C3776] 
RegulonDB:ECK120000680
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10687 EcoGene:EG10687]
[http://www.ncbi.nlm.nih.gov/gene?term=947501 GeneID:947501]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PARE ECOO157CYC:PARE] 
EchoBASE:EB0681
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33451 CGSC:33451] 
ASAP:ABE-0009950
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:par genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

parE

Mnemonic

Partition

Synonyms

ECK3021, b3030, JW2998, nfxD[1], nfxD

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Notes

Location(s) and DNA Sequence

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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

68.36 minutes 

MG1655: 3173418..3171526
<gbrowseImage> name=NC_000913:3171526..3173418 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3109568..3107676
<gbrowseImage> name=NC_012967:3107676..3109568 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3058674..3060566
<gbrowseImage> name=NC_012759:3058674..3060566 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3174052..3172160
<gbrowseImage> name=NC_007779:3172160..3174052 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3271163..3269271
<gbrowseImage> name=NC_010473:3269271..3271163 source=DH10B preset=GeneLocation </gbrowseImage>

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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
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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) Phenotype: Type Phenotype: Description Reference Availability Comments

parEL445H

L445H

(in strain: DH161; quinolone- resistant)

Strain variation; seeded from UniProt:P20083

parEC316Y

C316Y

Sensitivity to

temperature sensitivity

PMID:12509418[2]

identical to wt TopoIV in the superhelical DNA relaxation assay at permissive temperature

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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

JW2998

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCACGCAAACTTATAACGCTGA

Primer 2:CCAACCTCAATCTCCGCCATGTC

17B2

Kohara Phage

Genobase

PMID:3038334[4]

6B12

Kohara Phage

Genobase

PMID:3038334[4]

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[5]

est. P1 cotransduction: 46% [6]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[5]

est. P1 cotransduction: 80% [6]

plex5BA-parEC

Plasmid Clone

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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:EG10687

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10687

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000680

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947501

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0681

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009950

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Nurse, P et al. (2003) Topoisomerase III can serve as the cellular decatenase in Escherichia coli. J. Biol. Chem. 278 8653-60 PubMed
  3. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  4. ↑ 4.0 4.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Mossessova, E et al. (2000) Mutational analysis of Escherichia coli topoisomerase IV. I. Selection of dominant-negative parE alleles. J. Biol. Chem. 275 4099-103 PubMed

Categories

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