cfa: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="B46a9cbf84a6ab"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''cfa''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''cfa''
Cyclopropane fatty acid
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1657, b1661, JW1653, cdfA''<ref name='LIB:Riley_2006'/>, cdfA''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13889.B46a9cbf84a6ab&page=13889&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1657, b1661, JW1653, cdfA''<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="D46a9cbf8c5b32"  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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37.49 minutes&nbsp;
37.49 minutes&nbsp;
|
|
MG1655: 1739437..1740585<br />{{GBrowseFigureByCoord|1738437|1741585|ecoli|MG1655}}
MG1655: 1739437..1740585<br /><gbrowseImage>
name=NC_000913:1739437..1740585
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11531 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11531 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1738437..1741585 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1738437|1741585|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1739437..1740585&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1739437|1740585|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11531 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11531 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 1718680..1719828<br /><gbrowseImage>
name=NC_012967:1718680..1719828
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1718680|1719828|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1718680|1719828|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1631496..1632644<br /><gbrowseImage>
name=NC_012759:1631496..1632644
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1631496|1632644|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1631496|1632644|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1743127..1744275<br />{{GBrowseFigureByCoord|1742127|1745275|ecoli_W3110|W3110}}  
W3110: 1743127..1744275<br /><gbrowseImage>
name=NC_007779:1743127..1744275
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1742127|1745275|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|1743127|1744275|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1830008..1831156<br /><gbrowseImage>
name=NC_010473:1830008..1831156
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1742127..1745275 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1827712|1833452|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1743127..1744275&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1827712|1833452|FASTA Dump}}
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===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
1739440
|
Edman degradation
|
PMID:1445840<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="L46a9cbf9b9baf"  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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|
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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=107688 CGSC9407]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107688 CGSC9407]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0005555 cfa::Tn5KAN-2] (FB20416)
|
Insertion at nt 635 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20416]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0005555 cfa::Tn5KAN-2] (FB20417)
|
Insertion at nt 635 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20417]
|
contains [[pKD46]]
|-  
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|
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|
|
   
   
|-
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''cfa-2''
|
|
|
|
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PMID:6092874 PMID:3519583
|
[[cgscmutation:17027|CGSC:17027]]
|
|-
|
''cfa-3''
|
|
|
|
|
PMID:3519583 PMID:6092874
|
[[cgscmutation:17030|CGSC:17030]]
|
|-
|
''cfa-4''
|
|
|
|
|
PMID:3519583 PMID:6092874
|
[[cgscmutation:17032|CGSC:17032]]
|
|-
|
''cfa-5::kan''
|
|
|
|


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PMID:10411742 PMID:3038679
|
[[cgscmutation:64828|CGSC:64828]]
|
|-
|
''cfa-0''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:73935|CGSC:73935]]
|
|-
|
''&#916;cfa-739::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100276|CGSC:100276]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==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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!Resource!!Resource Type!!Source!!Notes/Reference
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JW1653
JW1653
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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:CCGCGAGCCACTCGAAGGCCGTT  
Primer 2:CCGCGAGCCACTCGAAGGCCGTT  
|-
|-
|
[[:Category:Kohara_Phage:4H6|4H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=318 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:13H4|13H4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=319 Genobase]
|
PMID:3038334
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[[yddE:Gene|zdd-235::Tn10]]
[[yddE:Gene|zdd-235::Tn10]]
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CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zdc-235::Tn10  
Synonyms:zdc-235::Tn10  
|-
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|
|
zdi-925::Tn10
zdi-925::Tn10
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CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<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:zdh-925::Tn10


Synonyms:zdh-925::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11531 EcoCyc:EG11531] 
EcoCyc:EG11531
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1493 EchoBASE:EB1493] 
EcoGene:EG11531
|
|
''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=b1661 EcoliGenExpDB:b1661] 
RegulonDB:ECK120001485
|
|
''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=C2055 ECOL199310CYC:C2055]
[http://www.ncbi.nlm.nih.gov/gene?term=944811 GeneID:944811]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11531 EcoGene:EG11531] 
EchoBASE:EB1493
|
|
''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=CFA ECOO157CYC:CFA] 
ASAP:ABE-0005555
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/10810 CGSC:10810] 
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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:cfa genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:38, 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

cfa

Mnemonic

Cyclopropane fatty acid

Synonyms

ECK1657, b1661, JW1653, cdfA[1], cdfA

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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

37.49 minutes 

MG1655: 1739437..1740585
<gbrowseImage> name=NC_000913:1739437..1740585 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1718680..1719828
<gbrowseImage> name=NC_012967:1718680..1719828 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1631496..1632644
<gbrowseImage> name=NC_012759:1631496..1632644 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1743127..1744275
<gbrowseImage> name=NC_007779:1743127..1744275 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1830008..1831156
<gbrowseImage> name=NC_010473:1830008..1831156 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

Coding Start (SO:0000323)

MG1655

1739440

Edman degradation

PMID:1445840[2]


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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

Δcfa (Keio:JW1653)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9407[4]

cfa::Tn5KAN-2 (FB20416)

Insertion at nt 635 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20416

does not contain pKD46

cfa::Tn5KAN-2 (FB20417)

Insertion at nt 635 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20417

contains pKD46

cfa-1

CGSC:10811

cfa-2

PMID:6092874[6] PMID:3519583[7]

CGSC:17027

cfa-3

PMID:3519583[7] PMID:6092874[6]

CGSC:17030

cfa-4

PMID:3519583[7] PMID:6092874[6]

CGSC:17032

cfa-5::kan

PMID:10411742[8] PMID:3038679[9]

CGSC:64828

cfa-0

CGSC:73935

Δcfa-739::kan

PMID:16738554[3]

CGSC:100276


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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

JW1653

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCAGTTCATCGTGTATAGAAGA

Primer 2:CCGCGAGCCACTCGAAGGCCGTT

4H6

Kohara Phage

Genobase

PMID:3038334[11]

13H4

Kohara Phage

Genobase

PMID:3038334[11]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: % [12]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[4]

est. P1 cotransduction: 21% [12]
Synonyms:zdh-925::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:EG11531

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11531

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001485

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944811

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1493

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005555

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. ↑ Wang, AY et al. (1992) Cyclopropane fatty acid synthase of Escherichia coli: deduced amino acid sequence, purification, and studies of the enzyme active site. Biochemistry 31 11020-8 PubMed
  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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 6.2 Grogan, DW & Cronan, JE Jr (1984) Genetic characterization of the Escherichia coli cyclopropane fatty acid (cfa) locus and neighboring loci. Mol. Gen. Genet. 196 367-72 PubMed
  7. ↑ 7.0 7.1 7.2 Grogan, DW & Cronan, JE Jr (1986) Characterization of Escherichia coli mutants completely defective in synthesis of cyclopropane fatty acids. J. Bacteriol. 166 872-7 PubMed
  8. ↑ Chang, YY & Cronan, JE Jr (1999) Membrane cyclopropane fatty acid content is a major factor in acid resistance of Escherichia coli. Mol. Microbiol. 33 249-59 PubMed
  9. ↑ Fellay, R et al. (1987) Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria. Gene 52 147-54 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 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
  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).

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