fruA: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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{|   id="K46a9d7974290e"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''fruA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''fruA''
Fructose
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2160, b2167, JW2154, ptsF''<ref name='LIB:Riley_2006'/>, ptsF''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14895.K46a9d7974290e&page=14895&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2160, b2167, JW2154, ptsF''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9d797bf283"  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
|-
|-  
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MG1655
MG1655
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48.66 minutes&nbsp;
48.66 minutes&nbsp;
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MG1655: 2259432..2257741<br />{{GBrowseFigureByCoord|2256741|2260432|ecoli|MG1655}}
MG1655: 2259432..2257741<br /><gbrowseImage>
name=NC_000913:2257741..2259432
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10336 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10336 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2256741..2260432 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2256741|2260432|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2257741..2259432&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2257741|2259432|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10336 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10336 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2212598..2210907<br /><gbrowseImage>
name=NC_012967:2210907..2212598
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2210907|2212598|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2210907|2212598|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2150224..2151915<br /><gbrowseImage>
name=NC_012759:2150224..2151915
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2150224|2151915|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2150224|2151915|FASTA Dump}}
|-  
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2264744..2263053<br />{{GBrowseFigureByCoord|2262053|2265744|ecoli_W3110|W3110}}
W3110: 2264744..2263053<br /><gbrowseImage>
name=NC_007779:2263053..2264744
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2262053..2265744 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2262053|2265744|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2263053..2264744&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2263053|2264744|FASTA Dump}}
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[[DH10B]]
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|
DH10B: 2350421..2348730<br /><gbrowseImage>
name=NC_010473:2348730..2350421
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2345348|2353803|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2345348|2353803|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="U46a9d79874dd6"  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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<protect><!--Sequence_notes--></protect>
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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="O46a9d798b9b33"  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
|-
|-  
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&Delta;fruA (Keio:JW2154)
''fruA(del)'' (Keio:JW2154)
|
|
deletion
deletion
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]   
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=108028 CGSC9747]<ref name='LIB:cgsc'/>  
|
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007172 fruA::Tn5KAN-2] (FB20664)
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Insertion at nt 236 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20664]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007172 fruA::Tn5KAN-2] (FB20665)
|
Insertion at nt 236 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20665]
|
does not contain [[pKD46]]
|-
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''fruA5''
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|
 
|
 
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[[cgscmutation:6118|CGSC:6118]]
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|-
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''fruA3''
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|
 
|
 
|
 
|
 
|
[[cgscmutation:6126|CGSC:6126]]
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|-
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''fruA10''
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|
 
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|
 
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[[cgscmutation:8969|CGSC:8969]]
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|-
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''fruA0''
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|
 
|
 
|
 
|
 
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[[cgscmutation:10763|CGSC:10763]]
|
   
|-
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''fruA9''
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|
 
|
 
|
 
|
 
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[[cgscmutation:12040|CGSC:12040]]
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|
   
   
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''fruA4''
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|
 
|
 
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[[cgscmutation:16086|CGSC:16086]]
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|-
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''fruA723(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101018|CGSC:101018]]
|
|-
|
''ptsF<sup>  -</sup>''
|
 
|
 
|
Resistant to
|
Resistant to sorbose
|
PMID:7028117
|
AS 1
|
table 1
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
A homologous recombination using various digestive enzymes allowed the mutant allele, fruA2 to be derived.The initial transformant colonies were selected in the presence of both thiostrepton and apramycin. ''Fru''A is specifically involved in fructose catabolism. A nonpolar ''fru''A mutation impairs growth on fructose and also leads to a constitutive low expression of the ''fru'' operon. Uptake and phosphorylation of frustose to fructose-1-phosphate by ''fru''A is necessary to relieve repression by fruR<ref name='PMID:15901699 '/>.


==Genetic Interactions==
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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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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2154
JW2154
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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:CCgGCTGCTTTCGCTACTGCGTC  
Primer 2:CCgGCTGCTTTCGCTACTGCGTC  
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[[:Category:Kohara_Phage:4F2|4F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=368 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12C12|12C12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=369 Genobase]
|
PMID:3038334
|-
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[[gatY:Gene|zbd-3104::Tn10]]
|
Linked marker
|
CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
|-
|
[[napA:Gene|napA722::Tn10]]
|
Linked marker
|
CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 15% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zeg-722, zei-722::Tn10
 
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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=EG10336 EcoCyc:EG10336] 
EcoCyc:EG10336
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0332 EchoBASE:EB0332] 
EcoGene:EG10336
|
|
''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=b2167 EcoliGenExpDB:b2167] 
RegulonDB:ECK120000330
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|
''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=C2702 ECOL199310CYC:C2702]
[http://www.ncbi.nlm.nih.gov/gene?term=946672 GeneID:946672]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
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[http://ecogene.org/geneinfo.php?eg_id=EG10336 EcoGene:EG10336] 
EchoBASE:EB0332
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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=FRUA ECOO157CYC:FRUA] 
ASAP:ABE-0007172
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/350 CGSC:350] 
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:fru genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

fruA

Mnemonic

Fructose

Synonyms

ECK2160, b2167, JW2154, ptsF[1], ptsF

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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

48.66 minutes 

MG1655: 2259432..2257741
<gbrowseImage> name=NC_000913:2257741..2259432 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2212598..2210907
<gbrowseImage> name=NC_012967:2210907..2212598 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2150224..2151915
<gbrowseImage> name=NC_012759:2150224..2151915 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2264744..2263053
<gbrowseImage> name=NC_007779:2263053..2264744 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2350421..2348730
<gbrowseImage> name=NC_010473:2348730..2350421 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

fruA(del) (Keio:JW2154)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC9747[3]

fruA::Tn5KAN-2 (FB20664)

Insertion at nt 236 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20664

contains pKD46

fruA::Tn5KAN-2 (FB20665)

Insertion at nt 236 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20665

does not contain pKD46

fruA5

CGSC:6118

fruA3

CGSC:6126

fruA10

CGSC:8969

fruA0

CGSC:10763

fruA9

CGSC:12040

fruA4

CGSC:16086

fruA723(del)::kan

PMID:16738554[2]

CGSC:101018

ptsF -

Resistant to

Resistant to sorbose

PMID:7028117[5]

AS 1

table 1

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Notes

A homologous recombination using various digestive enzymes allowed the mutant allele, fruA2 to be derived.The initial transformant colonies were selected in the presence of both thiostrepton and apramycin. FruA is specifically involved in fructose catabolism. A nonpolar fruA mutation impairs growth on fructose and also leads to a constitutive low expression of the fru operon. Uptake and phosphorylation of frustose to fructose-1-phosphate by fruA is necessary to relieve repression by fruR[6].


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

JW2154

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAAAACGCTGCTGATTATTGA

Primer 2:CCgGCTGCTTTCGCTACTGCGTC

4F2

Kohara Phage

Genobase

PMID:3038334[8]

12C12

Kohara Phage

Genobase

PMID:3038334[8]

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[3]

est. P1 cotransduction: % [9]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[3]

est. P1 cotransduction: 15% [9]
Synonyms:zeg-722, zei-722::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:EG10336

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10336

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000330

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946672

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0332

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007172

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Slater, AC et al. (1981) L-Sorbose phosphorylation in Escherichia coli K-12. Biochim. Biophys. Acta 646 365-7 PubMed
  6. ↑ Barrière, C et al. (2005) Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. J. Bacteriol. 187 3752-61 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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