ppk:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
imported>WikiEntryBot
Automated import of articles
 
touch
 
(53 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<!--PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE, YOU'RE PROBABLY IN THE WRONG PLACE-->
<!--
***************************************************************************************************************************************************
*
*              PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE,
*                            YOU'RE PROBABLY IN THE WRONG PLACE
*
*
***************************************************************************************************************************************************
-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ppk}}{{Tab On|Gene|ppk}}{{Tab|Gene Product(s)|ppk}}{{Tab|Expression|ppk}}{{Tab|Evolution|ppk}}{{Tab|On One Page|ppk}}{{TabsBottom}}
{{Tab|Quickview|ppk}}{{Tab On|Gene|ppk}}{{Tab|Gene Product(s)|ppk}}{{Tab|Expression|ppk}}{{Tab|Evolution|ppk}}{{Tab|On One Page|ppk}}{{TabsBottom}}
Line 6: Line 14:
|{{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]]
Line 15: Line 25:
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faca9510b1-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.S46a9df7d87146-->
{|{{Prettytable}}
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|  id="S46a9df7d87146"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ppk''  
''ppk''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Polyphosphate kinase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2497, b2501, JW2486''<ref name='LIB:Riley_2006'/>, JW2486''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.S46a9df7d87146&page=15569&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK2497, b2501, JW2486''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..E469faca9510b1&page=&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faca9510b1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.S46a9df7d87146-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 40: Line 58:


==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
<!--box uid=421aa90e079fa326b6494f812ad13e79..K469faca99856e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.M46a9df7e1088a-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='19498'
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_location_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9df7e1088a"  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
Line 52: Line 76:
56.49 minutes, 56.49 minutes&nbsp;
56.49 minutes, 56.49 minutes&nbsp;
|
|
MG1655: 2621066..2623132<br />{{GBrowseFigureByCoord|2620066|2624132|ecoli|MG1655}}
MG1655: 2621066..2623132<br /><gbrowseImage>
name=NC_000913:2621066..2623132
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11510 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11510 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2620066..2624132 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2620066|2624132|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2621066..2623132&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2621066|2623132|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11510 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11510 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2543863..2545929<br /><gbrowseImage>
name=NC_012967:2543863..2545929
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2543863|2545929|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2543863|2545929|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2506871..2508937<br /><gbrowseImage>
name=NC_012759:2506871..2508937
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2506871|2508937|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2506871|2508937|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 66: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 2621700..2623766<br />{{GBrowseFigureByCoord|2620700|2624766|ecoli_W3110|W3110}}  
W3110: 2621700..2623766<br /><gbrowseImage>
name=NC_007779:2621700..2623766
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2620700|2624766|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2620700..2624766 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|2621700|2623766|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2621700..2623766&plugin_action=Go FASTA Dump]
[[DH10B]]
|-class='sortbottom'
|
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..K469faca99856e&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
 
|
DH10B: 2712831..2714897<br /><gbrowseImage>
name=NC_010473:2712831..2714897
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2708699|2719029|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2708699|2719029|FASTA Dump}}
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.M46a9df7e1088a&page=15569&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..K469faca99856e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.M46a9df7e1088a-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 81: Line 164:


==Sequence Features==
==Sequence Features==
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faca9b3b3e-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.P46a9df7ebd652-->
{|class = 'sortable' {{Prettytable}} id='19499'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_sequence_features_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a9df7ebd652"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..E469faca9b3b3e&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
2621069
|
Edman degradation
|
PMID:1331061<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.P46a9df7ebd652&page=15569&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faca9b3b3e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.P46a9df7ebd652-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 96: Line 199:


==Alleles and Phenotypes==
==Alleles and Phenotypes==
<!--box uid=421aa90e079fa326b6494f812ad13e79..L469faca9bea22-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.R46a9df7f0f4b9-->
{|class = 'sortable' {{Prettytable}} id='19500'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_alleles_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9df7f0f4b9"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!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'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..L469faca9bea22&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|
&Delta;ppk (Keio:JW2486)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108266 CGSC9985]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008235 ppk::Tn5KAN-2] (FB20830)
|
Insertion at nt 1370 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20830]
|
contains [[pKD46]]
|-
|
&Delta;ppk::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;ppk::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;ppk::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Asparagine]]
|
PMID:16095938
|
 
|
|-
|
''&#916;ppk-749::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102436|CGSC:102436]]
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.R46a9df7f0f4b9&page=15569&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..L469faca9bea22-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.R46a9df7f0f4b9-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15569.O4e04c16135a27-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O4e04c16135a27"  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.15569.O4e04c16135a27&page=15569&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15569.O4e04c16135a27--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
<!--box uid=421aa90e079fa326b6494f812ad13e79..F469faca9c98ca-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.A46a9df7fbc4ff-->
{|class = 'sortable' {{Prettytable}} id='19501'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9df7fbc4ff"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
|-  
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..F469faca9c98ca&page=&pagename={{FULLPAGENAMEE}} edit table] || || ||
|
JW2486
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGGTCAGGAAAAGCTATACAT
 
Primer 2:CCTTCAGGTTGTTCGAGTGATTT
|-
|
[[:Category:Kohara_Phage:10H6|10H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=425 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5A11|5A11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=426 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8E3|8E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=427 Genobase]
|
PMID:3038334
|-
|
[[purC:Gene|purC80::Tn10]]
|
Linked marker
|
CAG18470 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38904 CGSC7413]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[hcaT:Gene|zfh-208::Tn10]]
|
Linked marker
|
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 16% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zff-208::Tn10
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.A46a9df7fbc4ff&page=15569&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..F469faca9c98ca-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.A46a9df7fbc4ff-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 126: Line 428:


==Accessions in Other Databases==
==Accessions in Other Databases==
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faca9d4750-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.C46a9df805df63-->
{|class = 'sortable' {{Prettytable}} id='19502'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9df805df63"  class=" tableEdit Gene_accessions_table" 
|- {{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=EG11510 EcoCyc:EG11510] 
EcoCyc:EG11510
|
|
''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=EB1472 EchoBASE:EB1472] 
EcoGene:EG11510
|
|
''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=b2501 EcoliGenExpDB:b2501] 
RegulonDB:ECK120001466
|
|
''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=C3019 ECOL199310CYC:C3019]
[http://www.ncbi.nlm.nih.gov/gene?term=946971 GeneID:946971]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11510 EcoGene:EG11510] 
EchoBASE:EB1472
|
|
''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=PPK ECOO157CYC:PPK] 
ASAP:ABE-0008235
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.C46a9df805df63&page=15569&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/32894 CGSC:32894] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..G469faca9d4750&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faca9d4750-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.C46a9df805df63-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 190: Line 492:


==Links==
==Links==
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.Y46a6fc55e90f3-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a6fc55e90f3"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
!|Name!!URL!!Comments
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15569.Y46a6fc55e90f3&page=15569&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15569.Y46a6fc55e90f3-->




<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:ppk genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

ppk

Mnemonic

Polyphosphate kinase

Synonyms

ECK2497, b2501, JW2486[1], JW2486

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

56.49 minutes, 56.49 minutes 

MG1655: 2621066..2623132
<gbrowseImage> name=NC_000913:2621066..2623132 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2543863..2545929
<gbrowseImage> name=NC_012967:2543863..2545929 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2506871..2508937
<gbrowseImage> name=NC_012759:2506871..2508937 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2621700..2623766
<gbrowseImage> name=NC_007779:2621700..2623766 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2712831..2714897
<gbrowseImage> name=NC_010473:2712831..2714897 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

2621069

Edman degradation

PMID:1331061[2]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

Δppk (Keio:JW2486)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9985[4]

ppk::Tn5KAN-2 (FB20830)

Insertion at nt 1370 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20830

contains pKD46

Δppk::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[6]

Δppk::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[6]

Δppk::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[6]

Δppk-749::kan

PMID:16738554[3]

CGSC:102436


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2486

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGGTCAGGAAAAGCTATACAT

Primer 2:CCTTCAGGTTGTTCGAGTGATTT

10H6

Kohara Phage

Genobase

PMID:3038334[8]

5A11

Kohara Phage

Genobase

PMID:3038334[8]

8E3

Kohara Phage

Genobase

PMID:3038334[8]

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[4]

est. P1 cotransduction: 35% [9]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[4]

est. P1 cotransduction: 16% [9]
Synonyms:zff-208::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11510

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11510

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001466

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946971

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1472

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008235

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Akiyama, M et al. (1992) The polyphosphate kinase gene of Escherichia coli. Isolation and sequence of the ppk gene and membrane location of the protein. J. Biol. Chem. 267 22556-61 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 6.2 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ppk:Gene&oldid=1478957"