pgk:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|pgk}}{{Tab On|Gene|pgk}}{{Tab|Gene Product(s)|pgk}}{{Tab|Expression|pgk}}{{Tab|Evolution|pgk}}{{Tab|On One Page|pgk}}{{TabsBottom}}
{{Tab|Quickview|pgk}}{{Tab On|Gene|pgk}}{{Tab|Gene Product(s)|pgk}}{{Tab|Expression|pgk}}{{Tab|Evolution|pgk}}{{Tab|On One Page|pgk}}{{TabsBottom}}
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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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''pgk''  
''pgk''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Phosphoglycerate kinase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2922, b2926, JW2893''<ref name='LIB:Riley_2006'/>, JW2893''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16419.G46a9e98d67b9a&page=16419&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2922, b2926, JW2893''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<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="R46a9e98de6e14"  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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66.16 minutes&nbsp;
66.16 minutes&nbsp;
|
|
MG1655: 3070644..3069481<br />{{GBrowseFigureByCoord|3068481|3071644|ecoli|MG1655}}
MG1655: 3070644..3069481<br /><gbrowseImage>
name=NC_000913:3069481..3070644
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10703 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10703 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3068481..3071644 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3068481|3071644|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3069481..3070644&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3069481|3070644|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10703 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10703 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2958373..2957210<br /><gbrowseImage>
name=NC_012967:2957210..2958373
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2957210|2958373|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2957210|2958373|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2956629..2957792<br /><gbrowseImage>
name=NC_012759:2956629..2957792
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2956629|2957792|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2956629|2957792|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3071278..3070115<br />{{GBrowseFigureByCoord|3069115|3072278|ecoli_W3110|W3110}}
W3110: 3071278..3070115<br /><gbrowseImage>
name=NC_007779:3070115..3071278
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3069115..3072278 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3069115|3072278|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3070115..3071278&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3070115|3071278|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3164514..3163351<br /><gbrowseImage>
name=NC_010473:3163351..3164514
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3161025|3166840|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3161025|3166840|FASTA Dump}}
 
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<!--Location_notes--></protect>
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9e98ea352b"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3069484
|
Edman degradation
|
PMID:9298646<br />PMID:9600841<br />PMID:9732527<br />PMID:9740056<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9e98eea8c8"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009605 pgk::Tn5KAN-I-SceI] (FB20977)
|
Insertion at nt 880 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20977]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009605 pgk::Tn5KAN-I-SceI] (FB20978)
|
Insertion at nt 880 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20978]
|
contains [[pKD46]]
|-
|
''pgk-2''
|
 
|
 
|
 
|
 
|
PMID:368027
|
[[cgscmutation:8944|CGSC:8944]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V4e04c0f3110da"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9e98fa753e"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2893
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCTCTGTAATTAAGATGACCGA
 
Primer 2:CCtTTCTTAGCGCGCTCTTCGAG
|-
|
[[:Category:Kohara_Phage:6C5|6C5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=472 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1H10|1H10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=473 Genobase]
|
PMID:3038334
|-
|
[[recD:Gene|recD1901::Tn10]]
|
Linked marker
|
CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[speA:Gene|speA210::Tn10]]
|
Linked marker
|
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 57% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9e9904c36e"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10703 EcoCyc:EG10703] 
EcoCyc:EG10703
|
|
''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=EB0697 EchoBASE:EB0697] 
EcoGene:EG10703
|
|
''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=b2926 EcoliGenExpDB:b2926] 
RegulonDB:ECK120000695
|
|
''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=C3504 ECOL199310CYC:C3504]
[http://www.ncbi.nlm.nih.gov/gene?term=947414 GeneID:947414]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10703 EcoGene:EG10703] 
EchoBASE:EB0697
|
|
''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=G7E-3 ECOO157CYC:G7E-3] 
ASAP:ABE-0009605
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16419.C46a9e9904c36e&page=16419&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/408 CGSC:408] 
|
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{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==Links==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:pgk 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

pgk

Mnemonic

Phosphoglycerate kinase

Synonyms

ECK2922, b2926, JW2893[1], JW2893

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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

66.16 minutes 

MG1655: 3070644..3069481
<gbrowseImage> name=NC_000913:3069481..3070644 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2958373..2957210
<gbrowseImage> name=NC_012967:2957210..2958373 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2956629..2957792
<gbrowseImage> name=NC_012759:2956629..2957792 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3071278..3070115
<gbrowseImage> name=NC_007779:3070115..3071278 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3164514..3163351
<gbrowseImage> name=NC_010473:3163351..3164514 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

3069484

Edman degradation

PMID:9298646[2]
PMID:9600841[3]
PMID:9732527[4]
PMID:9740056[5]


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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

pgk::Tn5KAN-I-SceI (FB20977)

Insertion at nt 880 in Plus orientation

PMID:15262929[6]

E. coli Genome Project:FB20977

does not contain pKD46

pgk::Tn5KAN-I-SceI (FB20978)

Insertion at nt 880 in Plus orientation

PMID:15262929[6]

E. coli Genome Project:FB20978

contains pKD46

pgk-2

PMID:368027[7]

CGSC:8944


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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

JW2893

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCTCTGTAATTAAGATGACCGA

Primer 2:CCtTTCTTAGCGCGCTCTTCGAG

6C5

Kohara Phage

Genobase

PMID:3038334[9]

1H10

Kohara Phage

Genobase

PMID:3038334[9]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[10]

est. P1 cotransduction: % [11]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[10]

est. P1 cotransduction: 57% [11]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10703

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10703

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000695

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947414

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0697

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009605

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  4. ↑ Rompf, A et al. (1998) Changes in protein synthesis as a consequence of heme depletion in Escherichia coli. Curr. Microbiol. 37 226-30 PubMed
  5. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  6. ↑ 6.0 6.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ Thomson, J et al. (1979) ColE1 hybrid plasmids for Escherichia coli genes of glycolysis and the hexose monophosphate shunt. J. Bacteriol. 137 502-6 PubMed
  8. ↑ 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
  9. ↑ 9.0 9.1 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
  10. ↑ 10.0 10.1 CGSC: The Coli Genetics Stock Center
  11. ↑ 11.0 11.1 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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