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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*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="V46a9fdaa9804c" class=" tableEdit Gene_nomenclature_table"


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


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|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="B46a9fdab261cd"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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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]
{{GBrowseLink|ecoli|NC_000913|3918259|3921074|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3918259|3921074|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3919259|3920074|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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&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}}  
|-
|
[[DH10B]]
|
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3713630|3716445|GBrowse(W3110)}}
DH10B: 4017658..4016843<br /><gbrowseImage>
name=NC_010473:4016843..4017658
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3714630|3715445|FASTA Dump}}  
{{GBrowseLink|DH10B|NC_010473|4015213|4019288|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4015213|4019288|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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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="F46a9fdabde415"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|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="D46a9fdac34181"  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
|-
|
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]
|-  
|-  
|
|
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18037.W4e04b7fc2ee3d-->
<!--
******************************************************************************************
*
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W4e04b7fc2ee3d"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18037.W4e04b7fc2ee3d&page=18037&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18037.W4e04b7fc2ee3d--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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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="J46a9fdacec190"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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
|-  
|-  
|
|
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Synonyms:zie-296::Tn10  
Synonyms:zie-296::Tn10  


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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;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|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]
|
|-
|
[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]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3738 EcoliGenExpDB:b3738]
EcoCyc:EG10099
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4666 ECOL199310CYC:C4666]
EcoGene:EG10099
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10099 EcoGene:EG10099]
RegulonDB:ECK120000095
|
|
''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=ATPB ECOO157CYC:ATPB]
[http://www.ncbi.nlm.nih.gov/gene?term=948252 GeneID:948252]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/32 CGSC:32]
EchoBASE:EB0097
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012222&formSubmitReturn=1 ASAP:ABE-0012222]
ASAP:ABE-0012222
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===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:atp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:49, 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

[back to top]


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

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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>

edit table


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).

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