ada: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="P46a9d8ad71d31"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ada''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ada''
Adaptive (response)
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2205, b2213, JW2201''<ref name='LIB:Riley_2006'/>, JW2201''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14985.P46a9d8ad71d31&page=14985&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2205, b2213, JW2201''<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="D46a9d8adeebbb"  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
|-
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MG1655
MG1655
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49.73 minutes&nbsp;
49.73 minutes&nbsp;
|
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MG1655: 2308427..2307363<br />{{GBrowseFigureByCoord|2306363|2309427|ecoli|MG1655}}
MG1655: 2308427..2307363<br /><gbrowseImage>
name=NC_000913:2307363..2308427
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10029 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10029 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2306363..2309427 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2306363|2309427|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2307363..2308427&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2307363|2308427|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10029 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10029 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2260509..2259445<br /><gbrowseImage>
name=NC_012967:2259445..2260509
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2259445|2260509|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2259445|2260509|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2193168..2194232<br /><gbrowseImage>
name=NC_012759:2193168..2194232
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2193168|2194232|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2193168|2194232|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2313739..2312675<br />{{GBrowseFigureByCoord|2311675|2314739|ecoli_W3110|W3110}}  
W3110: 2313739..2312675<br /><gbrowseImage>
name=NC_007779:2312675..2313739
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2311675|2314739|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|2312675|2313739|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2399415..2398351<br /><gbrowseImage>
name=NC_010473:2398351..2399415
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2311675..2314739 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2396223|2401543|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2312675..2313739&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2396223|2401543|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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Coding Start (SO:0000323)
|
[[MG1655]]
|
2307363
|
Edman degradation
|
PMID:2987251<br />
|
 
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<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====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="Z46a9d8aee9980"  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
|-
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adaE75D
|
|
E75D
|
|
(in strain: B)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P06134 UniProt:P06134]
|-
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adaAQ79PR
|
|
AQ79PR
|
|
(in strain: B)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P06134 UniProt:P06134]
|-
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adaI318V
|
|
I318V
|
|
(in strain: B)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P06134 UniProt:P06134]
|-
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adaT330S
|
|
T330S
|
|
(in strain: B)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P06134 UniProt:P06134]
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108061 CGSC9780]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108061 CGSC9780]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007311 ada::Tn5KAN-2] (FB20708)
|
Insertion at nt 687 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20708]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007311 ada::Tn5KAN-2] (FB20709)
|
Insertion at nt 687 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20709]
|
contains [[pKD46]]
|-  
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''&#916;ada-766::kan''
''ada-766(del)::kan''
|
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:99908|CGSC:99908]]
[[cgscmutation:99908|CGSC:99908]]
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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
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2201
JW2201
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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
Line 306: Line 507:


Primer 2:CCtCTCTCCTCATTTTCAGCTTC  
Primer 2:CCtCTCTCCTCATTTTCAGCTTC  
|-
|-
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[[:Category:Kohara_Phage:22A6|22A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=373 Genobase]
|
PMID:3038334
|-  
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[[napA:Gene|napA722::Tn10]]
[[napA:Gene|napA722::Tn10]]
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CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zeg-722, zei-722::Tn10  
Synonyms:zeg-722, zei-722::Tn10  
|-
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|
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[[atoS:Gene|atoS298::Tn10]]
[[atoS:Gene|atoS298::Tn10]]
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CAG12177 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44154 CGSC7525]<ref name='LIB:cgsc'/>
CAG12177 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44154 CGSC7525]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 65% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 65% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).
Synonyms:zeh-298::Tn10, zej-298::Tn10  
 


The original CAG12177 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).
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===Notes===
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG10029 EcoCyc:EG10029]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0028 EchoBASE:EB0028]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2213 EcoliGenExpDB:b2213]
EcoCyc:EG10029
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2754 ECOL199310CYC:C2754]
EcoGene:EG10029
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10029 EcoGene:EG10029]
RegulonDB:ECK120000026
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=ADA ECOO157CYC:ADA]
[http://www.ncbi.nlm.nih.gov/gene?term=946710 GeneID:946710]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
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|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1043 CGSC:1043]
EchoBASE:EB0028
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007311&formSubmitReturn=1 ASAP:ABE-0007311] 
ASAP:ABE-0007311
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
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[[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:ada genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

ada

Mnemonic

Adaptive (response)

Synonyms

ECK2205, b2213, JW2201[1], JW2201

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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

49.73 minutes 

MG1655: 2308427..2307363
<gbrowseImage> name=NC_000913:2307363..2308427 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2260509..2259445
<gbrowseImage> name=NC_012967:2259445..2260509 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2193168..2194232
<gbrowseImage> name=NC_012759:2193168..2194232 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2313739..2312675
<gbrowseImage> name=NC_007779:2312675..2313739 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2399415..2398351
<gbrowseImage> name=NC_010473:2398351..2399415 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

2307363

Edman degradation

PMID:2987251[2]


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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

adaE75D

E75D

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaAQ79PR

AQ79PR

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaI318V

I318V

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaT330S

T330S

(in strain: B)

Strain variation; seeded from UniProt:P06134

Δada (Keio:JW2201)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9780[4]

ada::Tn5KAN-2 (FB20708)

Insertion at nt 687 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20708

does not contain pKD46

ada::Tn5KAN-2 (FB20709)

Insertion at nt 687 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20709

contains pKD46

ada-1

CGSC:12943

ada-2

CGSC:12946

ada-3

CGSC:12948

ada-4

CGSC:12950

ada-5

CGSC:12952

ada-6

CGSC:12954

ada-766(del)::kan

PMID:16738554[3]

CGSC:99908


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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

JW2201

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAAAAAAGCCACATGCTTAAC

Primer 2:CCtCTCTCCTCATTTTCAGCTTC

22A6

Kohara Phage

Genobase

PMID:3038334[7]

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[4]

est. P1 cotransduction: 82% [8]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[4]

est. P1 cotransduction: 65% [8]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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:EG10029

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10029

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000026

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946710

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0028

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007311

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. ↑ Nakabeppu, Y et al. (1985) Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase. J. Biol. Chem. 260 7281-8 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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 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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