parC: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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{|{{Prettytable}}
{| {{Prettytable}} id="C46a9eba98290f"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''parC''  
''parC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
partitioning of the nucleoid
partitioning of the nucleoid
Partition
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3010, b3019, JW2987''<ref name='LIB:Riley_2006'/>
''ECK3010, b3019, JW2987''<ref name='LIB:Riley_2006'/>, JW2987''
|-
 
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
The partitioning defect comes from the inability of these cells to partition the nucleoids into daughter cells.  This leads to filamented cells with a cluster of DNA and other DNA- free cells


==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
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{|class = 'sortable' {{Prettytable}} id='142982'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9ebaa0dd6c"  class=" tableEdit Gene_location_table" 
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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68.15 minutes&nbsp;
68.15 minutes&nbsp;
|
|
MG1655: 3163995..3161737<br />{{GBrowseFigureByCoord|3160737|3164995|ecoli|MG1655}}
MG1655: 3163995..3161737<br /><gbrowseImage>
name=NC_000913:3161737..3163995
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10686 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10686 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3160737..3164995 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3160737|3164995|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3161737..3163995&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3161737|3163995|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10686 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10686 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3100145..3097887<br /><gbrowseImage>
name=NC_012967:3097887..3100145
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3097887|3100145|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3097887|3100145|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3048885..3051143<br /><gbrowseImage>
name=NC_012759:3048885..3051143
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3048885|3051143|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3048885|3051143|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3164629..3162371<br />{{GBrowseFigureByCoord|3161371|3165629|ecoli_W3110|W3110}}  
W3110: 3164629..3162371<br /><gbrowseImage>
name=NC_007779:3162371..3164629
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3161371|3165629|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|3162371|3164629|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 3261740..3259482<br /><gbrowseImage>
name=NC_010473:3259482..3261740
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3161371..3165629 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3254966|3266256|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3162371..3164629&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3254966|3266256|FASTA Dump}}
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="K46a9ebab13e41"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
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''parC1215''
|
G2199A
|
G703D
|
Growth Phenotype
|
*ts @ 42
*Chromosome partitioning phenotype
*Filamentation
|
PMID:2170028, PMID:2842295
|
|
&Delta;parC (Keio:JW2987)
 
|
|
deletion
actual nucleotide mapping was referenced in  <ref name='PMID:2170028'/>
|-
|
|
deletion
''parC10''
|
|


|
Y120H
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
DNA nicking independent of ATP hydrolysis
|
PMID:9077455
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] 
 
|
|
   
   
|-
|-
|
''parC<sup>L80</sup>''
|
 
|
S80L
|
Resistant to
|
Quinolone resistance
|
PMID:8524852
|
 
|
The mutation conferred increased resistance toward quinolones, specifically norfloxcin. See figure 3.
chEBI:23765
|-  
|
|
parC1215
''parC<sup>L80</sup>'' ''gyrA<sup>r</sup>''
|
|


|
|
parC S80L
gyrA S83L


|
|
Growth Phenotype
Resistant to
|
|
ts @ 42
quinolone resistance
|
|
[[PMID:2170028]]<ref name=PMID:2170028/>, [[PMID:2842295]]<ref name=PMID:2842295/>
PMID:8524852
|
|


|
|
The double mutation conferred a 6 fold increase of quinolone resistance compared to the mutation with only the ''gyrA<sup>R</sup>'' mutation. See figure 4 for experimental results.
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chEBI:23765
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
*The partitioning defect comes from the inability of these cells to partition the nucleoids into daughter cells.  This results in filamentous cells with a cluster of nucleoid at the center and subsequent DNA-free cells.
*The Keio collection<ref name='PMID:16738554'/> lists a deletion of ''parC'', which is an essential gene.  There is a duplication of the ''parC'' region.<ref name='PMID:20029369'/>.
*Suppressors of the ''parC1215'' mutation when expressed at high-copy<ref name='PMID:12509418'/>:
**''topB''
**''dnaN'' (&beta; subunit of the DNA polymerase holoenzyme)
**''spcA'' (suppressor of ''parC'' A- will be renamed ''setB'')
==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes


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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW2987
JW2987
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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:CCtTCTTCGCTATCACCGCTGCT  
Primer 2:CCtTCTTCGCTATCACCGCTGCT  
|-
|-
|
[[:Category:Kohara_Phage:6H4|6H4]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=505 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:17B2|17B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=506 Genobase]
|
PMID:3038334
|-  
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[[metC:Gene|metC162::Tn10]]
[[metC:Gene|metC162::Tn10]]
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|
|
est. P1 cotransduction: 67% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 67% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[tolC:Gene|tolC210::Tn10]]
[[tolC:Gene|tolC210::Tn10]]
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|
|
est. P1 cotransduction: 56% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 56% <ref name='LIB:Nichols_linked_Tn'/>  
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plexBA-parEC
|
Plasmid Clone
|
 
|
*IPTG-inducible Topo IV expression plasmid<ref name='PMID:10660569'/> 
|-
|
pLC4-14
|
Plasmid Clone
|
plasmid from the Clarke-Carbon collection
|
PMID:2842295
 
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===Notes===
===Notes===
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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=EG10686 EcoCyc:EG10686] 
EcoCyc:EG10686
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0680 EchoBASE:EB0680] 
EcoGene:EG10686
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3019 EcoliGenExpDB:b3019] 
RegulonDB:ECK120000679
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3760 ECOL199310CYC:C3760]
[http://www.ncbi.nlm.nih.gov/gene?term=947499 GeneID:947499]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10686 EcoGene:EG10686] 
EchoBASE:EB0680
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PARC ECOO157CYC:PARC] 
ASAP:ABE-0009916
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16595.P46a9ebac6bc4d&page=16595&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33440 CGSC:33440] 
|
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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone 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

parC

Mnemonic

partitioning of the nucleoid Partition

Synonyms

ECK3010, b3019, JW2987[1], JW2987

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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

68.15 minutes 

MG1655: 3163995..3161737
<gbrowseImage> name=NC_000913:3161737..3163995 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3100145..3097887
<gbrowseImage> name=NC_012967:3097887..3100145 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3048885..3051143
<gbrowseImage> name=NC_012759:3048885..3051143 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3164629..3162371
<gbrowseImage> name=NC_007779:3162371..3164629 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3261740..3259482
<gbrowseImage> name=NC_010473:3259482..3261740 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

parC1215

G2199A

G703D

Growth Phenotype

  • ts @ 42
  • Chromosome partitioning phenotype
  • Filamentation

PMID:2170028[2], PMID:2842295[3]

actual nucleotide mapping was referenced in [2]

parC10

Y120H

DNA nicking independent of ATP hydrolysis

PMID:9077455[4]

parCL80

S80L

Resistant to

Quinolone resistance

PMID:8524852[5]

The mutation conferred increased resistance toward quinolones, specifically norfloxcin. See figure 3. chEBI:23765

parCL80 gyrAr

parC S80L gyrA S83L

Resistant to

quinolone resistance

PMID:8524852[5]

The double mutation conferred a 6 fold increase of quinolone resistance compared to the mutation with only the gyrAR mutation. See figure 4 for experimental results. chEBI:23765

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Notes

  • The partitioning defect comes from the inability of these cells to partition the nucleoids into daughter cells. This results in filamentous cells with a cluster of nucleoid at the center and subsequent DNA-free cells.
  • The Keio collection[6] lists a deletion of parC, which is an essential gene. There is a duplication of the parC region.[7].
  • Suppressors of the parC1215 mutation when expressed at high-copy[8]:
    • topB
    • dnaN (β subunit of the DNA polymerase holoenzyme)
    • spcA (suppressor of parC A- will be renamed setB)


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

JW2987

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCAGCGATATGGCAGAGCGCCT

Primer 2:CCtTCTTCGCTATCACCGCTGCT

6H4

Kohara Phage

Genobase

PMID:3038334[10]

17B2

Kohara Phage

Genobase

PMID:3038334[10]

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[11]

est. P1 cotransduction: 67% [12]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[11]

est. P1 cotransduction: 56% [12]

plexBA-parEC

Plasmid Clone

  • IPTG-inducible Topo IV expression plasmid[13]

pLC4-14

Plasmid Clone

plasmid from the Clarke-Carbon collection

PMID:2842295[3]

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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:EG10686

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10686

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000679

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947499

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0680

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009916

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. ↑ 2.0 2.1 Kato, J et al. (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell 63 393-404 PubMed
  3. ↑ 3.0 3.1 Kato, J et al. (1988) Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J. Bacteriol. 170 3967-77 PubMed
  4. ↑ Yokochi, T et al. (1996) DNA nicking by Escherichia coli topoisomerase IV with a substitution mutation from tyrosine to histidine at the active site. Genes Cells 1 1069-75 PubMed
  5. ↑ 5.0 5.1 Khodursky, AB et al. (1995) Topoisomerase IV is a target of quinolones in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 92 11801-5 PubMed
  6. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  7. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  8. ↑ Nurse, P et al. (2003) Topoisomerase III can serve as the cellular decatenase in Escherichia coli. J. Biol. Chem. 278 8653-60 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 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
  11. ↑ 11.0 11.1 CGSC: The Coli Genetics Stock Center
  12. ↑ 12.0 12.1 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).
  13. ↑ 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

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