arcB: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="H46a9f04eca5d5"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''arcB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''arcB''
Aerobic respiration control
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3200, b3210, JW5536''<ref name='LIB:Riley_2006'/>, JW5536''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16975.H46a9f04eca5d5&page=16975&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3200, b3210, JW5536''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='144126'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9f04f56393"  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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72.18 minutes&nbsp;
72.18 minutes&nbsp;
|
|
MG1655: 3351047..3348711<br />{{GBrowseFigureByCoord|3347711|3352047|ecoli|MG1655}}
MG1655: 3351047..3348711<br /><gbrowseImage>
name=NC_000913:3348711..3351047
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10062 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10062 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3347711..3352047 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3347711|3352047|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3348711..3351047&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3348711|3351047|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10062 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10062 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3288260..3285924<br /><gbrowseImage>
name=NC_012967:3285924..3288260
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3285924|3288260|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3285924|3288260|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3235859..3238195<br /><gbrowseImage>
name=NC_012759:3235859..3238195
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3235859|3238195|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3235859|3238195|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3352880..3350544<br />{{GBrowseFigureByCoord|3349544|3353880|ecoli_W3110|W3110}}
W3110: 3352880..3350544<br /><gbrowseImage>
name=NC_007779:3350544..3352880
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3349544..3353880 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3349544|3353880|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3350544..3352880&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3350544|3352880|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3448792..3446456<br /><gbrowseImage>
name=NC_010473:3446456..3448792
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3441784|3453464|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3441784|3453464|FASTA Dump}}
 
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===Notes===
===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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="D46a9f0505dc4c"  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;arcB (Keio:JW5536)
arcBH292Q
|
 
|
H292Q
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AEC3 UniProt:P0AEC3]
|-
|
arcBD576A
|
 
|
D576A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AEC3 UniProt:P0AEC3]
|-
|
arcBH717Q
|
 
|
H717Q
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AEC3 UniProt:P0AEC3]
|-
|
''arcB(del)'' (Keio:JW5536)
|
|
deletion
deletion
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=112244 CGSC11593]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=112244 CGSC11593]<ref name='LIB:cgsc'/>  
|
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|
|
[[PMID:10829079]]<ref name=PMID:10829079/>
PMID:10829079
|
|
[[cgscmutation:65938|CGSC:65938]]
[[cgscmutation:65938|CGSC:65938]]
Line 179: Line 294:


|
|
[[PMID:10829079]]<ref name=PMID:10829079/>
PMID:10829079
|
|
[[cgscmutation:65940|CGSC:65940]]
[[cgscmutation:65940|CGSC:65940]]
|
|
   
   
|-
|
''arcB738(del)''::kan
|


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|
 
|
 
|
PMID:16738554
|
[[cgscmutation:112242|CGSC:112242]]
|
|-
|
arcB1
|
 
|
ECL619
|
Growth Phenotype
|
Codependant with arcB2 for pilus formation
|
PMID:2565334
|
 
|
|-
|
arcB2
|
 
|
ECL620
|
Growth Phenotype
|
codependant with arcB1 for pilus formation
|
PMID:2565334
|
 
|
|-
|
CAG45114 ''arcB738(del)''::FRTKanFRT
|
Deletion
|
 
|
Sigma<sup>E</sup> activity
|
Increase in sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15364
|
See table S11 for full experimental results. 
 
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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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JW5536
JW5536
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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:cloned as old JW
Status:cloned as old JW
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Primer 2:CCTTTTTTAGTGGCTTTTGCCAC  
Primer 2:CCTTTTTTAGTGGCTTTTGCCAC  
|-
|-
|
[[:Category:Kohara_Phage:7E3|7E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=522 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3G10|3G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=523 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8D6|8D6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=524 Genobase]
|
PMID:3038334
|-  
|
|
[[sfsB:Gene|sfsB203::Tn10]]
[[sfsB:Gene|sfsB203::Tn10]]
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CAG12072 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38770 CGSC7440]<ref name='LIB:cgsc'/>
CAG12072 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38770 CGSC7440]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zgj-203::Tn10, zha-203::Tn10  
Synonyms:zgj-203::Tn10, zha-203::Tn10  
|-
|-  
|
|
[[yhcF:Gene|zhc-6::Tn10]]
[[yhcF:Gene|zhc-6::Tn10]]
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CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zha-6::Tn10


Synonyms:zha-6::Tn10
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===Notes===
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|- {{table_heading_style}}
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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=EG10062 EcoCyc:EG10062] 
EcoCyc:EG10062
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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=EB0060 EchoBASE:EB0060] 
EcoGene:EG10062
|
|
''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=b3210 EcoliGenExpDB:b3210] 
RegulonDB:ECK120000058
|
|
''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=C3970 ECOL199310CYC:C3970]
[http://www.ncbi.nlm.nih.gov/gene?term=947887 GeneID:947887]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10062 EcoGene:EG10062] 
EchoBASE:EB0060
|
|
''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=ARCB ECOO157CYC:ARCB] 
ASAP:ABE-0010537
|
|
''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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===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:arc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

arcB

Mnemonic

Aerobic respiration control

Synonyms

ECK3200, b3210, JW5536[1], JW5536

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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

72.18 minutes 

MG1655: 3351047..3348711
<gbrowseImage> name=NC_000913:3348711..3351047 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3288260..3285924
<gbrowseImage> name=NC_012967:3285924..3288260 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3235859..3238195
<gbrowseImage> name=NC_012759:3235859..3238195 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3352880..3350544
<gbrowseImage> name=NC_007779:3350544..3352880 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3448792..3446456
<gbrowseImage> name=NC_010473:3446456..3448792 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

arcBH292Q

H292Q

Loss of activity

seeded from UniProt:P0AEC3

arcBD576A

D576A

Loss of activity

seeded from UniProt:P0AEC3

arcBH717Q

H717Q

Loss of activity

seeded from UniProt:P0AEC3

arcB(del) (Keio:JW5536)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11593[3]

arcB41(del-ins,::FRT)

PMID:10829079[4]

CGSC:65938

arcB40(del-ins)::cat

PMID:10829079[4]

CGSC:65940

arcB738(del)::kan

PMID:16738554[2]

CGSC:112242

arcB1

ECL619

Growth Phenotype

Codependant with arcB2 for pilus formation

PMID:2565334[5]

arcB2

ECL620

Growth Phenotype

codependant with arcB1 for pilus formation

PMID:2565334[5]

CAG45114 arcB738(del)::FRTKanFRT

Deletion

SigmaE activity

Increase in sigmaE activity

PMID:23224554[6]

Parental Strain: CAG45114 Experimental Strain: SMR15364

See table S11 for full experimental results.

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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

JW5536

Plasmid clone

Shigen

PMID:16769691[7]

Status:cloned as old JW

Primer 1:GCCAAGCAAATTCGTCTGCTGGC

Primer 2:CCTTTTTTAGTGGCTTTTGCCAC

7E3

Kohara Phage

Genobase

PMID:3038334[8]

3G10

Kohara Phage

Genobase

PMID:3038334[8]

8D6

Kohara Phage

Genobase

PMID:3038334[8]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[3]

est. P1 cotransduction: 54% [9]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[3]

est. P1 cotransduction: 59% [9]
Synonyms:zha-6::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:EG10062

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10062

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000058

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947887

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0060

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010537

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Datsenko, KA & Wanner, BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97 6640-5 PubMed
  5. ↑ 5.0 5.1 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. ↑ 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 8.2 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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