grpE: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="T46a9e233bcb25"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''grpE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''grpE''
Growth after phage induction
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2610, b2614, JW2594''<ref name='LIB:Riley_2006'/>, JW2594''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15795.T46a9e233bcb25&page=15795&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2610, b2614, JW2594''<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="A46a9e23446ad6"  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
|-
|-  
|
|
MG1655
MG1655
Line 72: Line 76:
59.23 minutes&nbsp;
59.23 minutes&nbsp;
|
|
MG1655: 2748730..2748137<br />{{GBrowseFigureByCoord|2747137|2749730|ecoli|MG1655}}
MG1655: 2748730..2748137<br /><gbrowseImage>
name=NC_000913:2748137..2748730
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10416 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10416 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2747137|2749730|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2747137|2749730|GBrowse(MG1655)}}
   
   
|
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{{GBrowseFastaLink|ecoli|NC_000913|2748137|2748730|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2748137|2748730|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10416 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10416 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2672003..2671410<br /><gbrowseImage>
name=NC_012967:2671410..2672003
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2671410|2672003|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2671410|2672003|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2633949..2634542<br /><gbrowseImage>
name=NC_012759:2633949..2634542
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2633949|2634542|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2633949|2634542|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2749364..2748771<br />{{GBrowseFigureByCoord|2747771|2750364|ecoli_W3110|W3110}}  
W3110: 2749364..2748771<br /><gbrowseImage>
name=NC_007779:2748771..2749364
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2747771|2750364|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2748771|2749364|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2840495..2839902<br /><gbrowseImage>
name=NC_010473:2839902..2840495
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2747771|2750364|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|2838716|2841681|GBrowse(DH10B)}}
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2748771|2749364|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2838716|2841681|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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<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="Q46a9e23546ac2"  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!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
grpEV108A
|
|
V108A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEG122D
|
|
G122D
|
|
Temperature-sensitive phenotype
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEL149A
|
|
L149A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEQ155A
|
|
Q155A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEI157A
|
|
I157A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEM159A
|
|
M159A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEM174A
|
|
M174A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpER183A
|
|
R183A
|
|
Loss of ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpER186A
|
|
R186A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEM189A
|
|
M189A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEV192A
|
|
V192A
|
|
Loss of ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpER74A
|
|
R74A
|
|
Great decrease in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEP151A
|
|
P151A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpER73A
|
|
R73A
|
|
Great decrease in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEK82A
|
|
K82A
|
|
Great decrease in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEF86A
|
|
F86A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpER104A
|
|
R104A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-
|
grpEE107A
|
|
E107A
|
|
No effect in ability to interact with dnaK
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09372 UniProt:P09372]
|-  
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|
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|
|
[[PMID:2424889]]<ref name=PMID:2424889/>
PMID:2424889
|
|
[[cgscmutation:90840|CGSC:90840]]
[[cgscmutation:90840|CGSC:90840]]
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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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JW2594
JW2594
Line 180: Line 572:
[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 187: Line 579:


Primer 2:CCAGCTTTTGCTTTCGCTACAG  
Primer 2:CCAGCTTTTGCTTTCGCTACAG  
|-
|-
|
[[:Category:Kohara_Phage:E8F2|E8F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=438 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:22D7|22D7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=439 Genobase]
|
PMID:3038334
|-  
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[[pheA:Gene|pheA18::Tn10]]
[[pheA:Gene|pheA18::Tn10]]
Line 196: Line 606:
|
|
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[srlD:Gene|srlD3131::Tn10]]
[[srlD:Gene|srlD3131::Tn10]]
Line 204: Line 614:
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: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <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===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9e23698a64"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10416 EcoCyc:EG10416]
EcoCyc:EG10416
|
|
''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=EB0411 EchoBASE:EB0411]
EcoGene:EG10416
|
|
''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=b2614 EcoliGenExpDB:b2614]
RegulonDB:ECK120000409
|
|
''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]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3135 ECOL199310CYC:C3135]
[http://www.ncbi.nlm.nih.gov/gene?term=947097 GeneID:947097]
|
|
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=EG10416 EcoGene:EG10416]
EchoBASE:EB0411
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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=GRPE ECOO157CYC:GRPE]
ASAP:ABE-0008598
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''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/660 CGSC:660]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0008598&formSubmitReturn=1 ASAP:ABE-0008598]
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[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:grp genes]]
[[Category:grp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

grpE

Mnemonic

Growth after phage induction

Synonyms

ECK2610, b2614, JW2594[1], JW2594

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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

59.23 minutes 

MG1655: 2748730..2748137
<gbrowseImage> name=NC_000913:2748137..2748730 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2672003..2671410
<gbrowseImage> name=NC_012967:2671410..2672003 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2633949..2634542
<gbrowseImage> name=NC_012759:2633949..2634542 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2749364..2748771
<gbrowseImage> name=NC_007779:2748771..2749364 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2840495..2839902
<gbrowseImage> name=NC_010473:2839902..2840495 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

grpEV108A

V108A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEG122D

G122D

Temperature-sensitive phenotype

seeded from UniProt:P09372

grpEL149A

L149A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEQ155A

Q155A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEI157A

I157A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEM159A

M159A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEM174A

M174A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpER183A

R183A

Loss of ability to interact with dnaK

seeded from UniProt:P09372

grpER186A

R186A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEM189A

M189A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEV192A

V192A

Loss of ability to interact with dnaK

seeded from UniProt:P09372

grpER74A

R74A

Great decrease in ability to interact with dnaK

seeded from UniProt:P09372

grpEP151A

P151A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpER73A

R73A

Great decrease in ability to interact with dnaK

seeded from UniProt:P09372

grpEK82A

K82A

Great decrease in ability to interact with dnaK

seeded from UniProt:P09372

grpEF86A

F86A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpER104A

R104A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpEE107A

E107A

No effect in ability to interact with dnaK

seeded from UniProt:P09372

grpE280

PMID:2424889[2]

CGSC:90840


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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

JW2594

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAGTAGTAAAGAACAGAAAAC

Primer 2:CCAGCTTTTGCTTTCGCTACAG

E8F2

Kohara Phage

Genobase

PMID:3038334[4]

22D7

Kohara Phage

Genobase

PMID:3038334[4]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 69% [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: % [6]
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

EcoCyc

EcoCyc:EG10416

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10416

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000409

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947097

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0411

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008598

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. ↑ Ang, D et al. (1986) Escherichia coli grpE gene codes for heat shock protein B25.3, essential for both lambda DNA replication at all temperatures and host growth at high temperature. J. Bacteriol. 167 25-9 PubMed
  3. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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