atpB: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="V46a9fdaa9804c"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''atpB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''atpB''
ATP
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3731, b3738, JW3716, papD, uncB''<ref name='LIB:Riley_2006'/>, uncB''


|-
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!{{table_heading_style}} |Synonyms
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''ECK3731, b3738, JW3716, papD, uncB''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='147315'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9fdab261cd"  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
Line 72: Line 76:
84.47 minutes&nbsp;
84.47 minutes&nbsp;
|
|
MG1655: 3920074..3919259<br />{{GBrowseFigureByCoord|3918259|3921074|ecoli|MG1655}}
MG1655: 3920074..3919259<br /><gbrowseImage>
name=NC_000913:3919259..3920074
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10099 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10099 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3918259..3921074 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3918259|3921074|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3919259..3920074&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3919259|3920074|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10099 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10099 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3882417..3881602<br /><gbrowseImage>
name=NC_012967:3881602..3882417
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3881602|3882417|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3881602|3882417|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3807592..3808407<br /><gbrowseImage>
name=NC_012759:3807592..3808407
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3807592|3808407|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3807592|3808407|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3714630..3715445<br />{{GBrowseFigureByCoord|3713630|3716445|ecoli_W3110|W3110}}  
W3110: 3714630..3715445<br /><gbrowseImage>
name=NC_007779:3714630..3715445
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3713630|3716445|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3714630|3715445|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3713630..3716445 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3714630..3715445&plugin_action=Go FASTA Dump]
 
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DH10B: 4017658..4016843<br /><gbrowseImage>
name=NC_010473:4016843..4017658
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4015213|4019288|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4015213|4019288|FASTA Dump}}
 
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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="F46a9fdabde415"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="D46a9fdac34181"  class=" tableEdit Gene_allele_table dataTable" 
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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
|-
|-
|
atpBS206L
|
 
|
S206L
|
 
|
Reduced activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBL207Y,F
|
 
|
L207Y,F
|
 
|
No change in activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBR210K,I,V,E
|
 
|
R210K,I,V,E
|
 
|
Completely defective
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBA217R
|
 
|
A217R
|
 
|
Completely defective
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBH245Y
|
 
|
H245Y
|
 
|
Reduced activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBA217H
|
 
|
A217H
|
 
|
Reduced activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBN214V
|
 
|
N214V
|
 
|
Reduced activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-
|
atpBN214H
|
 
|
N214H
|
 
|
Completely defective
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AB98 UniProt:P0AB98]
|-  
|
|
&Delta;atpB (Keio:JW3716)
&Delta;atpB (Keio:JW3716)
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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=108998 CGSC10717]<ref name='LIB:cgsc'/>  
|
|-
|
''atpB402''
|
 
|
 
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
 
|
[[cgscmutation:7158|CGSC:7158]]
|
|
   
   
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|
''&#916;atpB767::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100136|CGSC:100136]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18037.W4e04b7fc2ee3d-->
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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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JW3716
JW3716
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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
Line 186: Line 443:


Primer 2:CCATGTTCTTCAGACGCCATCGA  
Primer 2:CCATGTTCTTCAGACGCCATCGA  
|-
|-
|
[[:Category:Kohara_Phage:2A1|2A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=560 Genobase]
|
PMID:3038334
|-  
|
|
zid-501::Tn10
zid-501::Tn10
Line 195: Line 461:
|
|
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[rbsA:Gene|rbsD296::Tn10]]
[[rbsA:Gene|rbsD296::Tn10]]
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CAG18501 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40333 CGSC7460]<ref name='LIB:cgsc'/>
CAG18501 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40333 CGSC7460]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zie-296::Tn10


Synonyms:zie-296::Tn10
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===Notes===
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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=EG10099 EcoCyc:EG10099] 
EcoCyc:EG10099
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|-  
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0097 EchoBASE:EB0097] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3738 EcoliGenExpDB:b3738] 
EcoGene:EG10099
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4666 ECOL199310CYC:C4666] 
RegulonDB:ECK120000095
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10099 EcoGene:EG10099]
[http://www.ncbi.nlm.nih.gov/gene?term=948252 GeneID:948252]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=ATPB ECOO157CYC:ATPB] 
EchoBASE:EB0097
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/32 CGSC:32] 
ASAP:ABE-0012222
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===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:atp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:49, 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

atpB

Mnemonic

ATP

Synonyms

ECK3731, b3738, JW3716, papD, uncB[1], uncB

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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

84.47 minutes 

MG1655: 3920074..3919259
<gbrowseImage> name=NC_000913:3919259..3920074 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3882417..3881602
<gbrowseImage> name=NC_012967:3881602..3882417 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3807592..3808407
<gbrowseImage> name=NC_012759:3807592..3808407 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3714630..3715445
<gbrowseImage> name=NC_007779:3714630..3715445 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4017658..4016843
<gbrowseImage> name=NC_010473:4016843..4017658 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

atpBS206L

S206L

Reduced activity

seeded from UniProt:P0AB98

atpBL207Y,F

L207Y,F

No change in activity

seeded from UniProt:P0AB98

atpBR210K,I,V,E

R210K,I,V,E

Completely defective

seeded from UniProt:P0AB98

atpBA217R

A217R

Completely defective

seeded from UniProt:P0AB98

atpBH245Y

H245Y

Reduced activity

seeded from UniProt:P0AB98

atpBA217H

A217H

Reduced activity

seeded from UniProt:P0AB98

atpBN214V

N214V

Reduced activity

seeded from UniProt:P0AB98

atpBN214H

N214H

Completely defective

seeded from UniProt:P0AB98

ΔatpB (Keio:JW3716)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10717[3]

atpB402

CGSC:7158

ΔatpB767::kan

PMID:16738554[2]

CGSC:100136


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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

JW3716

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCTTCAGAAAATATGACGCC

Primer 2:CCATGTTCTTCAGACGCCATCGA

2A1

Kohara Phage

Genobase

PMID:3038334[5]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[3]

est. P1 cotransduction: 14% [6]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[3]

est. P1 cotransduction: 70% [6]
Synonyms:zie-296::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:EG10099

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10099

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000095

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948252

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0097

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012222

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 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. ↑ 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
  5. ↑ 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
  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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