lhgO:Gene: Difference between revisions

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{{Tab|Quickview|ygaF}}{{Tab On|Gene|ygaF}}{{Tab|Gene Product(s)|ygaF}}{{Tab|Expression|ygaF}}{{Tab|Evolution|ygaF}}{{Tab|On One Page|ygaF}}{{TabsBottom}}
{{Tab|Quickview|lhgO}}{{Tab On|Gene|lhgO}}{{Tab|Gene Product(s)|lhgO}}{{Tab|Expression|lhgO}}{{Tab|Evolution|lhgO}}{{Tab|On One Page|lhgO}}{{TabsBottom}}
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|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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="A46a9e320714aa"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''lhgO''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ygaF''
L-2-HydroxyGlutarate Oxidase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2654, b2660, JW2635'', ygaF<ref name='LIB:Riley_2006'/>, JW2635, ygaF''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15883.A46a9e320714aa&page=15883&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2654, b2660, JW2635''<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="M46a9e320efc39"  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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60.09 minutes&nbsp;
60.09 minutes&nbsp;
|
|
MG1655: 2788004..2789272<br />{{GBrowseFigureByCoord|2787004|2790272|ecoli|MG1655}}
MG1655: 2788004..2789272<br /><gbrowseImage>
name=NC_000913:2788004..2789272
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12387 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12387 EcoCyc]
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|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2788004..2789272&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|2788004|2789272|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12387 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12387 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2684662..2685930<br /><gbrowseImage>
name=NC_012967:2684662..2685930
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2684662|2685930|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2684662|2685930|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2673816..2675084<br /><gbrowseImage>
name=NC_012759:2673816..2675084
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|2673816|NC_2675084|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|2673816|NC_2675084|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2788638..2789906<br />{{GBrowseFigureByCoord|2787638|2790906|ecoli_W3110|W3110}}  
W3110: 2788638..2789906<br /><gbrowseImage>
name=NC_007779:2788638..2789906
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|2787638|2790906|GBrowse(W3110)}}
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|2788638|2789906|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2879769..2881037<br /><gbrowseImage>
name=NC_010473:2879769..2881037
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2787638|2790906|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_DH10B|NC_010473|2877233|2883573|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2788638..2789906&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2877233|2883573|FASTA Dump}}
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|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15883.M46a9e320efc39&page=15883&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15883.M46a9e320efc39&page=15883&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='140846'
{|  id="N46a9e321aa15d"  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
|-class='sortbottom'
 
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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}}
{| {{Prettytable}}  id="F46a9e321f0867" class=" tableEdit Gene_allele_table dataTable"
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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|
|
[[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=108357 CGSC10076]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108357 CGSC10076]<ref name='LIB:cgsc'/>  
|
|-
|
&Delta;ygaF::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
|
|-
|
&Delta;ygaF::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Aspartate]]
|
PMID:16095938
|
|
|
   
   
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:104858|CGSC:104858]]
[[cgscmutation:104858|CGSC:104858]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15883.F46a9e321f0867&page=15883&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15883.Q4e04be617574f-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q4e04be617574f"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15883.Q4e04be617574f&page=15883&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW2635
JW2635
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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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTGATTAAATGCGGCGTGTAA  
Primer 2:CCTTGATTAAATGCGGCGTGTAA  
|-
|-
|
[[:Category:Kohara_Phage:12G12|12G12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=443 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10H9|10H9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=444 Genobase]
|
PMID:3038334
|-  
|
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[[pheA:Gene|pheA18::Tn10]]
[[pheA:Gene|pheA18::Tn10]]
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|
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est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[srlD:Gene|srlD3131::Tn10]]
[[srlD:Gene|srlD3131::Tn10]]
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CAG18642 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40097 CGSC7423]<ref name='LIB:cgsc'/>
CAG18642 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40097 CGSC7423]<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:zfh-3131::Tn10, zfi-3131::Tn10


Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
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===Notes===
===Notes===
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12387 EcoCyc:EG12387]
[http://chase.ou.edu/macro/searchlink.php?bnum=b2660 EcoliGenExpDB:b2660]
|
|
   
   
|-  
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2288 EchoBASE:EB2288]
[http://BioCyc.org/ECOL199310/new-image?object=C3208 ECOL199310CYC:C3208]
|
|
   
   
|-  
|-  
|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2660 EcoliGenExpDB:b2660]
[http://BioCyc.org/ECOO157/new-image?object=YGAF ECOO157CYC:YGAF]
|
|
   
   
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3208 ECOL199310CYC:C3208]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12387 ECOCYC:EG12387]
|
|
Escherichia coli str. K-12 substr. 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=EG12387 EcoGene:EG12387]
|
|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOO157/new-image?object=YGAF ECOO157CYC:YGAF]
[http://www.ncbi.nlm.nih.gov/gene?term=948069 GeneID:948069]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[RegulonDB]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0008756&formSubmitReturn=1 ASAP:ABE-0008756] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===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:yga genes]]
[[Category:yga genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:lhg genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

lhgO

Mnemonic

L-2-HydroxyGlutarate Oxidase

Synonyms

ECK2654, b2660, JW2635, ygaF[1], JW2635, ygaF

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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

60.09 minutes 

MG1655: 2788004..2789272
<gbrowseImage> name=NC_000913:2788004..2789272 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2684662..2685930
<gbrowseImage> name=NC_012967:2684662..2685930 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2673816..2675084
<gbrowseImage> name=NC_012759:2673816..2675084 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2788638..2789906
<gbrowseImage> name=NC_007779:2788638..2789906 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2879769..2881037
<gbrowseImage> name=NC_010473:2879769..2881037 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

ΔygaF (Keio:JW2635)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10076[3]

ΔygaF::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔygaF::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔygaF741::kan

PMID:16738554[2]

CGSC:104858


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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

JW2635

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTATGATTTTGTGATTATTGG

Primer 2:CCTTGATTAAATGCGGCGTGTAA

12G12

Kohara Phage

Genobase

PMID:3038334[6]

10H9

Kohara Phage

Genobase

PMID:3038334[6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[3]

est. P1 cotransduction: 9% [7]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[3]

est. P1 cotransduction: 21% [7]
Synonyms:zfh-3131::Tn10, zfi-3131::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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2660

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3208

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YGAF

EcoCyc (EcoliWiki Page)

ECOCYC:EG12387

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948069

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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 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 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  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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