kdpF:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|kdpF}}{{Tab On|Gene|kdpF}}{{Tab|Gene Product(s)|kdpF}}{{Tab|Expression|kdpF}}{{Tab|Evolution|kdpF}}{{Tab|On One Page|kdpF}}{{TabsBottom}}
{{Tab|Quickview|kdpF}}{{Tab On|Gene|kdpF}}{{Tab|Gene Product(s)|kdpF}}{{Tab|Expression|kdpF}}{{Tab|Evolution|kdpF}}{{Tab|On One Page|kdpF}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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{|   id="Q46a9b6c4139a4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''kdpF''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''kdpF''
K+- DePendence
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0687, b4513, JW0687''<ref name='LIB:Riley_2006'/>, JW0687''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11951.Q46a9b6c4139a4&page=11951&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0687, b4513, JW0687''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9b6c48be30"  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
|-
|-  
|
|
MG1655
MG1655
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15.69 minutes&nbsp;
15.69 minutes&nbsp;
|
|
MG1655: 728044..727955<br />{{GBrowseFigureByCoord|726955|729044|ecoli|MG1655}}
MG1655: 728044..727955<br /><gbrowseImage>
name=NC_000913:727955..728044
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10439 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10439 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:726955..729044 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|726955|729044|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:727955..728044&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|727955|728044|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10439 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10439 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 710916..710827<br /><gbrowseImage>
name=NC_012967:710827..710916
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|710827|710916|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|710827|710916|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 630715..630804<br /><gbrowseImage>
name=NC_012759:630715..630804
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|630715|630804|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|630715|630804|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 729243..729154<br />{{GBrowseFigureByCoord|728154|730243|ecoli_W3110|W3110}}  
W3110: 729243..729154<br /><gbrowseImage>
name=NC_007779:729154..729243
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|728154|730243|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|729154|729243|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:728154..730243 GBrowse(W3110)]
DH10B: 780636..780547<br /><gbrowseImage>
name=NC_010473:780547..780636
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:729154..729243&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|780369|780814|GBrowse(DH10B)}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b6c5343fa"  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====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9b6c573e47"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;kdpF (Keio:JW0687)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107049 CGSC8768]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;kdpF748::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101616|CGSC:101616]]
|
 
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<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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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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|
JW0687
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAGTGCAGGCGTGATAACCGG
 
Primer 2:CCGAACGCCTCCGCATTGATCAG
|-
|
[[:Category:Kohara_Phage:3G6|3G6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=174 Genobase]
|
PMID:3038334
|-
|
[[asnB:Gene|asnB3057::Tn10]]
|
Linked marker
|
CAG18433 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39394 CGSC7349]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
|-
|
[[nadA:Gene|nadA57::Tn10]]
|
Linked marker
|
CAG12147 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38017 CGSC7351]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G0-10439
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12126
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120016291
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10439 EcoCyc:G0-10439]
[http://www.ncbi.nlm.nih.gov/gene?term=948946 GeneID:948946]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2047 EchoBASE:EB2047] 
EchoBASE:EB2047
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12126 EcoGene:EG12126] 
ASAP:ABE-0285034
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:kdp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 19 September 2013

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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

kdpF

Mnemonic

K+- DePendence

Synonyms

ECK0687, b4513, JW0687[1], JW0687

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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

15.69 minutes 

MG1655: 728044..727955
<gbrowseImage> name=NC_000913:727955..728044 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 710916..710827
<gbrowseImage> name=NC_012967:710827..710916 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 630715..630804
<gbrowseImage> name=NC_012759:630715..630804 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 729243..729154
<gbrowseImage> name=NC_007779:729154..729243 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 780636..780547
<gbrowseImage> name=NC_010473:780547..780636 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

ΔkdpF (Keio:JW0687)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8768[3]

ΔkdpF748::kan

PMID:16738554[2]

CGSC:101616


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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

JW0687

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGTGCAGGCGTGATAACCGG

Primer 2:CCGAACGCCTCCGCATTGATCAG

3G6

Kohara Phage

Genobase

PMID:3038334[5]

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[3]

est. P1 cotransduction: 35% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[3]

est. P1 cotransduction: 9% [6]

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:G0-10439

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12126

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120016291

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948946

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2047

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0285034

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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