prc:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
imported>WikiEntryBot
Automated import of articles
touch
 
(61 intermediate revisions by 4 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|prc}}{{Tab On|Gene|prc}}{{Tab|Gene Product(s)|prc}}{{Tab|Expression|prc}}{{Tab|Evolution|prc}}{{Tab|On One Page|prc}}{{TabsBottom}}
{{Tab|Quickview|prc}}{{Tab On|Gene|prc}}{{Tab|Gene Product(s)|prc}}{{Tab|Expression|prc}}{{Tab|Evolution|prc}}{{Tab|On One Page|prc}}{{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..A469faa459b645-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfea1daa4-->
{|{{Prettytable}}
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|  id="S46a9cfea1daa4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''prc''  
''prc''
|-
!align=left {{table_heading_style}} |Mnemonic
||
PBP protease, C terminal
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1829, b1830, JW1819, tsp''<ref name='LIB:Riley_2006'/>, tsp''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfea1daa4&page=14233&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK1829, b1830, JW1819, tsp''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..A469faa459b645&page=&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..A469faa459b645-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfea1daa4-->
{{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..A469faa45e0e14-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.V46a9cfea99a44-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='15490'
******************************************************************************************
*
*  ** 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="V46a9cfea99a44"  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:
41.18 minutes&nbsp;
41.18 minutes&nbsp;
|
|
MG1655: 1912840..1910792<br />{{GBrowseFigureByCoord|1909792|1913840|ecoli|MG1655}}
MG1655: 1912840..1910792<br /><gbrowseImage>
name=NC_000913:1910792..1912840
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10760 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10760 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1909792..1913840 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1909792|1913840|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1910792..1912840&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1910792|1912840|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10760 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10760 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1893393..1891345<br /><gbrowseImage>
name=NC_012967:1891345..1893393
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1891345|1893393|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1891345|1893393|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1802851..1804899<br /><gbrowseImage>
name=NC_012759:1802851..1804899
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1802851|1804899|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1802851|1804899|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 66: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 1916530..1914482<br />{{GBrowseFigureByCoord|1913482|1917530|ecoli_W3110|W3110}}
W3110: 1916530..1914482<br /><gbrowseImage>
name=NC_007779:1914482..1916530
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1913482..1917530 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1913482|1917530|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1914482..1916530&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1914482|1916530|FASTA Dump}}
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..A469faa45e0e14&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|
[[DH10B]]
|
 
|
DH10B: 2003411..2001363<br /><gbrowseImage>
name=NC_010473:2001363..2003411
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1997267|2007507|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1997267|2007507|FASTA Dump}}
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.V46a9cfea99a44&page=14233&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..A469faa45e0e14-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.V46a9cfea99a44-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 81: Line 164:


==Sequence Features==
==Sequence Features==
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faa4602d79-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.Z46a9cfeb4c8a7-->
{|class = 'sortable' {{Prettytable}} id='15491'
<!--
******************************************************************************************
*
*  ** 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="Z46a9cfeb4c8a7"  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..E469faa4602d79&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
1910795
|
Edman degradation
|
PMID:1729701<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.Z46a9cfeb4c8a7&page=14233&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..E469faa4602d79-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.Z46a9cfeb4c8a7-->
{{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..I469faa460bb53-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.G46a9cfeb907b9-->
{|class = 'sortable' {{Prettytable}} id='15492'
<!--
******************************************************************************************
*
*  ** 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="G46a9cfeb907b9"  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
|-
|-
|
''prc(del)'' (Keio:JW1819)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=107801 CGSC9520]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006090 prc::Tn5KAN-2] (FB20464)
|
Insertion at nt 405 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20464]
|
contains [[pKD46]]
|-
|
prcK477R
|
 
|
K477R
|
 
|
Loss of activity. Perturbs protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcK477A,H
|
 
|
K477A,H
|
 
|
Loss of activity. No apparent effect on protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcG397A
|
 
|
G397A
|
 
|
Loss of activity. Perturbs protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcG398A
|
 
|
G398A
|
 
|
Loss of activity. Perturbs protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcS452A
|
 
|
S452A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcS452C
|
 
|
S452C
|
 
|
Reduces activity by over 90%
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcE455A
|
 
|
E455A
|
 
|
Loss of activity. Perturbs protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcD463A
|
 
|
D463A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcD463N
|
 
|
D463N
|
 
|
Reduces activity by 90%
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
prcT474A
|
 
|
T474A
|
 
|
Loss of activity. Perturbs protein structure
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P23865 UniProt:P23865]
|-
|
''prc-755(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102450|CGSC:102450]]
|
|-  
|
''prc755(del)''::FRT
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
Mutagenesis rate
|
|
&nbsp;
Decreased stress-induced mutagenesis (SIM) phenotype.
|
|
&nbsp;
PMID:23224554
|
|
&nbsp;
Parental Strain: SMR4562
 
Experimental Strain: SMR12251
|
|
&nbsp;
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..I469faa460bb53&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.G46a9cfeb907b9&page=14233&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..I469faa460bb53-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.G46a9cfeb907b9-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14233.F4e04c16c52d3b-->
<!--
******************************************************************************************
*
*  ** 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="F4e04c16c52d3b"  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.14233.F4e04c16c52d3b&page=14233&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14233.F4e04c16c52d3b--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faa46148f9-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.M46a9cfec43c85-->
{|class = 'sortable' {{Prettytable}} id='15493'
<!--
******************************************************************************************
*
*  ** 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="M46a9cfec43c85"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW1819
JW1819
Line 139: Line 504:
[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 146: Line 511:


Primer 2:CCtTTGACGGGAGCGGGTTGTTC  
Primer 2:CCtTTGACGGGAGCGGGTTGTTC  
|-class='sortbottom'
|-  
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..G469faa46148f9&page=&pagename={{FULLPAGENAMEE}} edit table] || || ||
|
[[:Category:Kohara_Phage:15D5|15D5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=335 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:19H3|19H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=336 Genobase]
|
PMID:3038334
|-
|
[[yeaI:Gene|zea-225::Tn10]]
|
Linked marker
|
CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 17% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdj-225::Tn10
|-
|
[[eda:Gene|eda-51::Tn10]]
|
Linked marker
|
CAG18486 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39983 CGSC7392]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.M46a9cfec43c85&page=14233&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faa46148f9-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.M46a9cfec43c85-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 156: Line 559:


==Accessions in Other Databases==
==Accessions in Other Databases==
<!--box uid=421aa90e079fa326b6494f812ad13e79..W469faa461d716-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfecd4be3-->
{|class = 'sortable' {{Prettytable}} id='15494'
<!--
******************************************************************************************
*
*  ** 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="S46a9cfecd4be3"  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=EG10760 EcoCyc:EG10760] 
EcoCyc:EG10760
|
|
''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=EB0753 EchoBASE:EB0753] 
EcoGene:EG10760
|
|
''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=b1830 EcoliGenExpDB:b1830] 
RegulonDB:ECK120000751
|
|
''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=C2239 ECOL199310CYC:C2239]
[http://www.ncbi.nlm.nih.gov/gene?term=946096 GeneID:946096]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10760 EcoGene:EG10760] 
EchoBASE:EB0753
|
|
''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=PRC ECOO157CYC:PRC] 
ASAP:ABE-0006090
|
|
''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=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfecd4be3&page=14233&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/32334 CGSC:32334] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..W469faa461d716&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..W469faa461d716-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.S46a9cfecd4be3-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 220: Line 623:


==Links==
==Links==
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='97952'
******************************************************************************************
|-
*
!
*  ** 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="E46a6ed48b4d15"  class=" tableEdit Links_table" 
|-class='sortbottom'
|- {{table_heading_style}}
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15&page=14233&pagename={{FULLPAGENAMEE}} edit table]
!|Name!!URL!!Comments
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15&page=14233&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14233.E46a6ed48b4d15-->


<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</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:prc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 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

prc

Mnemonic

PBP protease, C terminal

Synonyms

ECK1829, b1830, JW1819, tsp[1], tsp

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

41.18 minutes 

MG1655: 1912840..1910792
<gbrowseImage> name=NC_000913:1910792..1912840 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1893393..1891345
<gbrowseImage> name=NC_012967:1891345..1893393 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1802851..1804899
<gbrowseImage> name=NC_012759:1802851..1804899 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1916530..1914482
<gbrowseImage> name=NC_007779:1914482..1916530 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2003411..2001363
<gbrowseImage> name=NC_010473:2001363..2003411 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

1910795

Edman degradation

PMID:1729701[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

prc(del) (Keio:JW1819)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC9520[4]

prc::Tn5KAN-2 (FB20464)

Insertion at nt 405 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20464

contains pKD46

prcK477R

K477R

Loss of activity. Perturbs protein structure

seeded from UniProt:P23865

prcK477A,H

K477A,H

Loss of activity. No apparent effect on protein structure

seeded from UniProt:P23865

prcG397A

G397A

Loss of activity. Perturbs protein structure

seeded from UniProt:P23865

prcG398A

G398A

Loss of activity. Perturbs protein structure

seeded from UniProt:P23865

prcS452A

S452A

Loss of activity

seeded from UniProt:P23865

prcS452C

S452C

Reduces activity by over 90%

seeded from UniProt:P23865

prcE455A

E455A

Loss of activity. Perturbs protein structure

seeded from UniProt:P23865

prcD463A

D463A

Loss of activity

seeded from UniProt:P23865

prcD463N

D463N

Reduces activity by 90%

seeded from UniProt:P23865

prcT474A

T474A

Loss of activity. Perturbs protein structure

seeded from UniProt:P23865

prc-755(del)::kan

PMID:16738554[3]

CGSC:102450

prc755(del)::FRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[6]

Parental Strain: SMR4562

Experimental Strain: SMR12251

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

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

JW1819

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAACATGTTTTTTAGGCTTAC

Primer 2:CCtTTGACGGGAGCGGGTTGTTC

15D5

Kohara Phage

Genobase

PMID:3038334[8]

19H3

Kohara Phage

Genobase

PMID:3038334[8]

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[4]

est. P1 cotransduction: 17% [9]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[4]

est. P1 cotransduction: 50% [9]

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:EG10760

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10760

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000751

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946096

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0753

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006090

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. ↑ Silber, KR et al. (1992) Tsp: a tail-specific protease that selectively degrades proteins with nonpolar C termini. Proc. Natl. Acad. Sci. U.S.A. 89 295-9 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. ↑ 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 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=prc:Gene&oldid=1478290"