coaE: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="K46a9a8855d2c2"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''coaE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''coaE''
Coenzyme A
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0103, b0103, JW0100, yacE''<ref name='LIB:Riley_2006'/>, yacE''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10783.K46a9a8855d2c2&page=10783&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0103, b0103, JW0100, yacE''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125547'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9a885d97ae"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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2.43 minutes&nbsp;
2.43 minutes&nbsp;
|
|
MG1655: 113219..112599<br />{{GBrowseFigureByCoord|111599|114219|ecoli|MG1655}}
MG1655: 113219..112599<br /><gbrowseImage>
name=NC_000913:112599..113219
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12312 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12312 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:111599..114219 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|111599|114219|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:112599..113219&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|112599|113219|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12312 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12312 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 116023..115403<br /><gbrowseImage>
name=NC_012967:115403..116023
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|115403|116023|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|115403|116023|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 112598..113218<br /><gbrowseImage>
name=NC_012759:112598..113218
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|112598|113218|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|112598|113218|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 86: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 113219..112599<br />{{GBrowseFigureByCoord|111599|114219|ecoli_W3110|W3110}}  
W3110: 113219..112599<br /><gbrowseImage>
name=NC_007779:112599..113219
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|111599|114219|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|112599|113219|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 87323..86703<br /><gbrowseImage>
name=NC_010473:86703..87323
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:111599..114219 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|85463|88563|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:112599..113219&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|85463|88563|FASTA Dump}}
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===Notes===
===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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====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="Z46a9a886c3a26"  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
|-  
|-  
|
|
&Delta;coaE (Keio:JW0100)
''coaE(del)'' (Keio:JW0100)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
Strain contains duplication detected by PCR  PMID:18652654
|-
|
''yacE(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
''yacE(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
''yacE(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
 
|
|-
|
''yacE(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Succinate]]
|
PMID:16095938
|
 
|
|-
|
''yacE(del)''::kan
|
|
deletion
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
|
|-
|
''yacE(del)''::kan
|
|
deletion
deletion
|
|


|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Alanine]]
|
PMID:16095938
|
|
|-
|
''yacE(del)''::kan
|
deletion
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
[[Biolog]]:respiration
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106663 CGSC8382]<ref name='LIB:cgsc'/>
unable to respire [[Carbon sources|L-Asparagine]]
|
PMID:16095938
|
 
|
|
   
   
|-  
|-  
|
|
''ΔcoaE722::kan''
''yacE(del)''::kan
|
deletion
|
|


|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Aspartate]]
|
PMID:16095938
|
|
|-
|
''yacE(del)''::kan
|
deletion
|
|


|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Serine]]
|
PMID:16095938
|
|


|
|-
|
''coaE722(del)::kan''
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
 
|
 
|
 
|
PMID:16738554
|
|
[[cgscmutation:100358|CGSC:100358]]
[[cgscmutation:100358|CGSC:100358]]
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This allele appears to not exist in the Keio collection.  PCR analysis indicates an intact coaE gene in both JW0100 Keio strains.  
This allele appears to not exist in the Keio collection.  PCR analysis indicates an intact coaE gene in both JW0100 Keio strains.  


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10783.Z46a9a886c3a26&page=10783&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===
The Keio collection<ref name='PMID:16738554'/> lists a deletion of ''coaE''.  The insertion in this strain is a duplication of the ''coaE'' region.<ref name='PMID:20029369'/>
==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
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0100
JW0100
Line 197: Line 436:
[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
Line 204: Line 443:


Primer 2:CCCGGTTTTTCCTGTGAGACAAA  
Primer 2:CCCGGTTTTTCCTGTGAGACAAA  
|-
|-
|
[[:Category:Kohara_Phage:15B8|15B8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=111 Genobase]
|
PMID:3038334
|-  
|
|
leuO3051::Tn10
leuO3051::Tn10
Line 212: Line 460:
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  
Synonyms:zab-3051::Tn10  
|-  
 
 
The start of leuO was reannotated by Riley et al. (2006).  
|-
|
|
[[yadC:Gene|zad-220::Tn10]]
[[yadC:Gene|zad-220::Tn10]]
Line 227: Line 471:
|
|
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/>  
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===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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9a88801f1f"  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=EG12312 EcoCyc:EG12312]
EcoCyc:EG12312
|
|
''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=EB2218 EchoBASE:EB2218]
EcoGene:EG12312
|
|
''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=b0103 EcoliGenExpDB:b0103]
RegulonDB:ECK120002189
|
|
''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=C0123 ECOL199310CYC:C0123]
[http://www.ncbi.nlm.nih.gov/gene?term=949060 GeneID:949060]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12312 EcoGene:EG12312]
EchoBASE:EB2218
|
|
''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=YACE ECOO157CYC:YACE]
|
|
ASAP:ABE-0000357
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000357&formSubmitReturn=1 ASAP:ABE-0000357]
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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:coa genes]]
[[Category:coa genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 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

coaE

Mnemonic

Coenzyme A

Synonyms

ECK0103, b0103, JW0100, yacE[1], yacE

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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

2.43 minutes 

MG1655: 113219..112599
<gbrowseImage> name=NC_000913:112599..113219 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 116023..115403
<gbrowseImage> name=NC_012967:115403..116023 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 112598..113218
<gbrowseImage> name=NC_012759:112598..113218 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 113219..112599
<gbrowseImage> name=NC_007779:112599..113219 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 87323..86703
<gbrowseImage> name=NC_010473:86703..87323 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

coaE(del) (Keio:JW0100)

deletion

deletion

PMID:16738554[2]

Shigen

Strain contains duplication detected by PCR PMID:18652654[3]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

yacE(del)::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938[4]

coaE722(del)::kan

PMID:16738554[2]

CGSC:100358

This allele appears to not exist in the Keio collection. PCR analysis indicates an intact coaE gene in both JW0100 Keio strains.

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Notes

The Keio collection[2] lists a deletion of coaE. The insertion in this strain is a duplication of the coaE region.[5]


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

JW0100

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAGGTATATAGTTGCCTTAAC

Primer 2:CCCGGTTTTTCCTGTGAGACAAA

15B8

Kohara Phage

Genobase

PMID:3038334[7]

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[8]

est. P1 cotransduction: 32% [9]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[8]

est. P1 cotransduction: 23% [9]

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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:EG12312

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12312

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002189

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2218

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000357

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 2.2 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. ↑ Plaimas, K et al. (2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2 67 PubMed
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 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. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 CGSC: The Coli Genetics Stock Center
  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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