arcA: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="O46aa0ead3a0b4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''arcA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''arcA''
Aerobic respiration control
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4393, b4401, JW4364, dye, fexA, msp, seg, sfrA, cpxC''<ref name='LIB:Riley_2006'/>, cpxC''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19357.O46aa0ead3a0b4&page=19357&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK4393, b4401, JW4364, dye, fexA, msp, seg, sfrA, cpxC''<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="I46aa0eadc480c"  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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99.96 minutes&nbsp;
99.96 minutes&nbsp;
|
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MG1655: 4638329..4637613<br />{{GBrowseFigureByCoord|4636613|4639329|ecoli|MG1655}}
MG1655: 4638329..4637613<br /><gbrowseImage>
name=NC_000913:4637613..4638329
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10061 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10061 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4636613..4639329 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4636613|4639329|GBrowse(MG1655)}}
   
   
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4637613..4638329&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4637613|4638329|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10061 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10061 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 4628466..4627750<br /><gbrowseImage>
name=NC_012967:4627750..4628466
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4627750|4628466|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4627750|4628466|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4576097..4576813<br /><gbrowseImage>
name=NC_012759:4576097..4576813
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4576097|4576813|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|4576097|4576813|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 4644986..4644270<br />{{GBrowseFigureByCoord|4643270|4645986|ecoli_W3110|W3110}}  
W3110: 4644986..4644270<br /><gbrowseImage>
name=NC_007779:4644270..4644986
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4643270|4645986|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4643270..4645986 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|4644270|4644986|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4644270..4644986&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 4684791..4684075<br /><gbrowseImage>
name=NC_010473:4684075..4684791
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4682643|4686223|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4682643|4686223|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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Coding Start (SO:0000323)
|
[[MG1655]]
|
4637613
|
Edman degradation
|
PMID:9298646<br />
|
 
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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="K46aa0eaedc052"  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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&Delta;arcA (Keio:JW4364)
''arcA(del)'' (Keio:JW4364)
|
|
deletion
deletion
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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=109398 CGSC11117]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=109398 CGSC11117]<ref name='LIB:cgsc'/>  
|
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''&#916;arcA43''
''arcA43(del)''
|
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|-  
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''&#916;arcA45''
''arcA45(del)''
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|-  
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''&#916;arcA44::kan''
''arcA44:(del)'':kan
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|-  
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''&#916;arcA726::kan''
''arcA726(del)''::kan
|
|


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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100034|CGSC:100034]]
[[cgscmutation:100034|CGSC:100034]]
|
|
   
   
|-
|
arcA
|
mutation
|
mutation
|
|
represses aerobic function
|
PMID:2565334
|
|
|-
|
''arcA''(P)::Tn''10''dCam
|
|
|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
Experimental Strain: SMR12023
|
Mutation was comparatively weak with decrease only happening to 33-67% of population.
|-
|
CAG45114 ''arcA726(del)''::FRTKanFRT
|
deletion
|
|
Sigma<sup>E</sup> Activity
|
Decrease in Sigma<sup>E</sup> Activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain:SMR1360
|
See Table S11 for experimental Data
|-
|
CAG45114 ''arcA726(del)''::FRTKanFRT
|
Deletion
|


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Sigma<sup>E</sup> activity
|
Increase in sigma<sup>E</sup> activity
|
PMID23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15360
 
|
See table S11 for full experimental data
 
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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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JW4364
JW4364
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCATCTTCCAGATCACCGCAGAA  
Primer 2:CCATCTTCCAGATCACCGCAGAA  
|-
|-
|
[[:Category:Kohara_Phage:12A4|12A4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=675 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:15A5|15A5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=676 Genobase]
|
PMID:3038334
|-  
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[[mdoB:Gene|mdoB202::Tn10]]
[[mdoB:Gene|mdoB202::Tn10]]
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CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjj-202::Tn10, zji-202::Tn10  
Synonyms:zjj-202::Tn10, zji-202::Tn10  
|-
|-  
|
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[[thrA:Gene|thrA34::Tn10]]
[[thrA:Gene|thrA34::Tn10]]
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CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 93% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 93% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:thr-34::Tn10


Synonyms:thr-34::Tn10
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===Notes===
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!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=EG10061 EcoCyc:EG10061] 
EcoCyc:EG10061
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|
''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=EB0059 EchoBASE:EB0059] 
EcoGene:EG10061
|
|
''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=b4401 EcoliGenExpDB:b4401] 
RegulonDB:ECK120000057
|
|
''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=C5488 ECOL199310CYC:C5488]
[http://www.ncbi.nlm.nih.gov/gene?term=948874 GeneID:948874]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10061 EcoGene:EG10061] 
EchoBASE:EB0059
|
|
''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=ARCA ECOO157CYC:ARCA] 
ASAP:ABE-0014434
|
|
''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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===Notes===
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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:arc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:53, 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

arcA

Mnemonic

Aerobic respiration control

Synonyms

ECK4393, b4401, JW4364, dye, fexA, msp, seg, sfrA, cpxC[1], cpxC

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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

99.96 minutes 

MG1655: 4638329..4637613
<gbrowseImage> name=NC_000913:4637613..4638329 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4628466..4627750
<gbrowseImage> name=NC_012967:4627750..4628466 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4576097..4576813
<gbrowseImage> name=NC_012759:4576097..4576813 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4644986..4644270
<gbrowseImage> name=NC_007779:4644270..4644986 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4684791..4684075
<gbrowseImage> name=NC_010473:4684075..4684791 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

4637613

Edman degradation

PMID:9298646[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

arcA(del) (Keio:JW4364)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11117[4]

arcA43(del)

CGSC:78398

arcA45(del)

CGSC:79752

arcA44:(del):kan

CGSC:90811

arcA726(del)::kan

PMID:16738554[3]

CGSC:100034

arcA

mutation

mutation

represses aerobic function

PMID:2565334[5]

arcA(P)::Tn10dCam

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[6]

Parental Strain: SMR4562

Experimental Strain: SMR12023

Mutation was comparatively weak with decrease only happening to 33-67% of population.

CAG45114 arcA726(del)::FRTKanFRT

deletion

SigmaE Activity

Decrease in SigmaE Activity

PMID:23224554[6]

Parental Strain: CAG45114 Experimental Strain:SMR1360

See Table S11 for experimental Data

CAG45114 arcA726(del)::FRTKanFRT

Deletion

SigmaE activity

Increase in sigmaE activity

PMID23224554

Parental Strain: CAG45114 Experimental Strain: SMR15360

See table S11 for full experimental data

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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

JW4364

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCAGACCCCGCACATTCTTAT

Primer 2:CCATCTTCCAGATCACCGCAGAA

12A4

Kohara Phage

Genobase

PMID:3038334[8]

15A5

Kohara Phage

Genobase

PMID:3038334[8]

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[4]

est. P1 cotransduction: 14% [9]
Synonyms:zjj-202::Tn10, zji-202::Tn10

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 93% [9]
Synonyms:thr-34::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:EG10061

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10061

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000057

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948874

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0059

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014434

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. ↑ 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. ↑ 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. ↑ Iuchi, S et al. (1989) Differentiation of arcA, arcB, and cpxA mutant phenotypes of Escherichia coli by sex pilus formation and enzyme regulation. J. Bacteriol. 171 2889-93 PubMed
  6. ↑ 6.0 6.1 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  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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