cusA: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}}
{|   id="B46a9b3ce6555a"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''cusA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''cusA''
Cu sensor
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0567, b0575, JW0564, ybdE, agrA''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, silA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11711.B46a9b3ce6555a&page=11711&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0567, b0575, JW0564, ybdE, agrA''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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===Notes===
===Notes===
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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
Line 72: Line 76:
12.89 minutes&nbsp;
12.89 minutes&nbsp;
|
|
MG1655: 597937..601080<br />{{GBrowseFigureByCoord|596937|602080|ecoli|MG1655}}
MG1655: 597937..601080<br /><gbrowseImage>
name=NC_000913:597937..601080
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12367 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12367 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:596937..602080 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|596937|602080|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:597937..601080&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|597937|601080|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12367 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12367 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 579617..582760<br /><gbrowseImage>
name=NC_012967:579617..582760
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|579617|582760|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|579617|582760|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 500697..503840<br /><gbrowseImage>
name=NC_012759:500697..503840
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|500697|503840|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|500697|503840|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 597937..601080<br />{{GBrowseFigureByCoord|596937|602080|ecoli_W3110|W3110}}  
W3110: 597937..601080<br /><gbrowseImage>
name=NC_007779:597937..601080
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|596937|602080|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|597937|601080|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 537269..540412<br /><gbrowseImage>
name=NC_010473:537269..540412
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:596937..602080 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|530983|546698|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:597937..601080&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|530983|546698|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 650529..653672<br /><gbrowseImage>
name=NC_010473:650529..653672
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|644243|659958|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|644243|659958|FASTA Dump}}
 
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===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!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="V46a9b3cfc5a2f"  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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cusAM755I
|
 
|
M755I
|
 
|
Slight decrease in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
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cusAM792I
|
 
|
M792I
|
 
|
No change in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
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cusAM812I
|
 
|
M812I
|
 
|
Slight decrease in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
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cusAM833I
|
 
|
M833I
|
 
|
Slight decrease in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAM640I
|
 
|
M640I
|
 
|
No change in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAM672I
|
 
|
M672I
|
 
|
Loss of copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAM738I
|
 
|
M738I
|
 
|
No change in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAE412Q
|
 
|
E412Q
|
 
|
Loss of copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAM573I
|
 
|
M573I
|
 
|
Loss of copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAM623I
|
 
|
M623I
|
 
|
Loss of copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAA399D
|
 
|
A399D
|
 
|
Strong decrease in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAD405N
|
 
|
D405N
|
 
|
Loss of copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-
|
cusAE412D
|
 
|
E412D
|
 
|
Slight decrease in copper resistance
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P38054 UniProt:P38054]
|-  
|
|
&Delta;cusA (Keio:JW0564)
&Delta;cusA (Keio:JW0564)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106970 CGSC8689]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106970 CGSC8689]<ref name='LIB:cgsc'/>  
|
|
   
   
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''&#916;cusA784::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100438|CGSC:100438]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0564
JW0564
Line 179: Line 520:
[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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
Line 186: Line 527:


Primer 2:CCTTTCCGTACCCGATGTCGGTG  
Primer 2:CCTTTCCGTACCCGATGTCGGTG  
|-
|-
|
[[:Category:Kohara_Phage:2F5|2F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=162 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:21A9S|21A9S]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=163 Genobase]
|
PMID:3038334
|-  
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[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
Line 194: Line 553:
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  
|-
|-  
|
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[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
Line 205: Line 563:
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 21% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 21% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbd-601::Tn10, zbe-601::Tn10


Synonyms:zbd-601::Tn10, zbe-601::Tn10
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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=EG12367 EcoCyc:EG12367] 
EcoCyc:EG12367
|
|
''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=EB2270 EchoBASE:EB2270] 
EcoGene:EG12367
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0575 EcoliGenExpDB:b0575] 
RegulonDB:ECK120002235
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C0661 ECOL199310CYC:C0661]
[http://www.ncbi.nlm.nih.gov/gene?term=945191 GeneID:945191]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12367 EcoGene:EG12367] 
EchoBASE:EB2270
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=YBDE ECOO157CYC:YBDE] 
ASAP:ABE-0001971
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
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[[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:cus genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 19 September 2013

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

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

cusA

Mnemonic

Cu sensor

Synonyms

ECK0567, b0575, JW0564, ybdE, agrA[1][2], silA

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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

12.89 minutes 

MG1655: 597937..601080
<gbrowseImage> name=NC_000913:597937..601080 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 579617..582760
<gbrowseImage> name=NC_012967:579617..582760 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 500697..503840
<gbrowseImage> name=NC_012759:500697..503840 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 597937..601080
<gbrowseImage> name=NC_007779:597937..601080 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 537269..540412
<gbrowseImage> name=NC_010473:537269..540412 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 650529..653672
<gbrowseImage> name=NC_010473:650529..653672 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

cusAM755I

M755I

Slight decrease in copper resistance

seeded from UniProt:P38054

cusAM792I

M792I

No change in copper resistance

seeded from UniProt:P38054

cusAM812I

M812I

Slight decrease in copper resistance

seeded from UniProt:P38054

cusAM833I

M833I

Slight decrease in copper resistance

seeded from UniProt:P38054

cusAM640I

M640I

No change in copper resistance

seeded from UniProt:P38054

cusAM672I

M672I

Loss of copper resistance

seeded from UniProt:P38054

cusAM738I

M738I

No change in copper resistance

seeded from UniProt:P38054

cusAE412Q

E412Q

Loss of copper resistance

seeded from UniProt:P38054

cusAM573I

M573I

Loss of copper resistance

seeded from UniProt:P38054

cusAM623I

M623I

Loss of copper resistance

seeded from UniProt:P38054

cusAA399D

A399D

Strong decrease in copper resistance

seeded from UniProt:P38054

cusAD405N

D405N

Loss of copper resistance

seeded from UniProt:P38054

cusAE412D

E412D

Slight decrease in copper resistance

seeded from UniProt:P38054

ΔcusA (Keio:JW0564)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8689[4]

ΔcusA784::kan

PMID:16738554[3]

CGSC:100438


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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

JW0564

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCATTGAATGGATTATTCGTCG

Primer 2:CCTTTCCGTACCCGATGTCGGTG

2F5

Kohara Phage

Genobase

PMID:3038334[6]

21A9S

Kohara Phage

Genobase

PMID:3038334[6]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[4]

est. P1 cotransduction: 13% [7]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[4]

est. P1 cotransduction: 21% [7]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

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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:EG12367

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12367

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002235

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945191

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2270

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001971

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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).

Categories

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