ttdB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
edited by 127.0.0.1 via TableEdit
touch
 
(44 intermediate revisions by 3 users not shown)
Line 14: 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 21: Line 23:
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|{{Prettytable}}
******************************************************************************************
*
*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|   id="A46a9ecad29505"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ttdB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ttdB''
Tartrate dehydratase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3052, b3062, JW3034, ygjB''<ref name='LIB:Riley_2006'/>, ygjB''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505&page=16679&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK3052, b3062, JW3034, ygjB''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505&page=16679&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.A46a9ecad29505-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 53: Line 61:
<protect>
<protect>
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='143235'
******************************************************************************************
*
*  ** 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="M46a9ecada8deb"  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 63: Line 76:
69.09 minutes&nbsp;
69.09 minutes&nbsp;
|
|
MG1655: 3205393..3205998<br />{{GBrowseFigureByCoord|3204393|3206998|ecoli|MG1655}}
MG1655: 3205393..3205998<br /><gbrowseImage>
name=NC_000913:3205393..3205998
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11169 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11169 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3204393..3206998 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3204393|3206998|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3205393..3205998&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3205393|3205998|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11169 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11169 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3140188..3140793<br /><gbrowseImage>
name=NC_012967:3140188..3140793
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3140188|3140793|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3140188|3140793|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3092541..3093146<br /><gbrowseImage>
name=NC_012759:3092541..3093146
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3092541|3093146|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3092541|3093146|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 77: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 3206027..3206632<br />{{GBrowseFigureByCoord|3205027|3207632|ecoli_W3110|W3110}}
W3110: 3206027..3206632<br /><gbrowseImage>
name=NC_007779:3206027..3206632
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3205027..3207632 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3205027|3207632|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3206027..3206632&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3206027|3206632|FASTA Dump}}
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb&page=16679&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|
[[DH10B]]
|
 
|
DH10B: 3303138..3303743<br /><gbrowseImage>
name=NC_010473:3303138..3303743
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3301928|3304953|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3301928|3304953|FASTA Dump}}
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb&page=16679&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.M46a9ecada8deb-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 94: Line 166:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='143236'
******************************************************************************************
*
*  ** 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="J46a9ecae66dcf"  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=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf&page=16679&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf&page=16679&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.J46a9ecae66dcf-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 110: Line 188:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='143237'
******************************************************************************************
*
*  ** 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="C46a9ecaeaecbb"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
|
|
&Delta;ttdB (Keio:JW3034)
&Delta;ttdB (Keio:JW3034)
Line 126: Line 209:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108599 CGSC10318]<ref name='LIB:cgsc'/>
|
|
   
   
|-class='sortbottom'
|-  
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb&page=16679&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010052 ttdB::Tn5KAN-I-SceI] (FB21016)
|
Insertion at nt 142 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21016]
|
contains [[pKD46]]
|-
|
''&#916;ttdB754::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:103252|CGSC:103252]]
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb&page=16679&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.C46a9ecaeaecbb-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16679.Z4e04c50dd370e-->
<!--
******************************************************************************************
*
*  ** 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="Z4e04c50dd370e"  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.16679.Z4e04c50dd370e&page=16679&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16679.Z4e04c50dd370e--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='143238'
******************************************************************************************
*
*  ** 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="N46a9ecaf6cdee"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW3034
JW3034
Line 153: Line 300:
[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 160: Line 307:


Primer 2:CCTTTGATGTAATGGACGTGCTC  
Primer 2:CCTTTGATGTAATGGACGTGCTC  
|-class='sortbottom'
|-  
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee&page=16679&pagename={{FULLPAGENAMEE}} edit table] || || ||
|
[[:Category:Kohara_Phage:19F2|19F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=509 Genobase]
|
PMID:3038334
|-
|
[[tolC:Gene|tolC210::Tn10]]
|
Linked marker
|
CAG12184 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38758 CGSC7437]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[aer:Gene|aer-3075::Tn10]]
|
Linked marker
|
CAG12152 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38761 CGSC7438]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 71% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee&page=16679&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.N46a9ecaf6cdee-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 172: Line 348:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='143239'
******************************************************************************************
*
*  ** 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="F46a9ecb0134fe"  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=EG11169 EcoCyc:EG11169] 
EcoCyc:EG11169
|
|
''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=EB1157 EchoBASE:EB1157] 
EcoGene:EG11169
|
|
''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=b3062 EcoliGenExpDB:b3062] 
RegulonDB:ECK120001152
|
|
''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=C3813 ECOL199310CYC:C3813]
[http://www.ncbi.nlm.nih.gov/gene?term=947568 GeneID:947568]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11169 EcoGene:EG11169] 
EchoBASE:EB1157
|
|
''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=TTDB ECOO157CYC:TTDB] 
ASAP:ABE-0010052
|
|
''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=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe&page=16679&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33462 CGSC:33462] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe&page=16679&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.F46a9ecb0134fe-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 237: Line 412:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='99172'
******************************************************************************************
*
*  ** 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="Q46a70873c456d"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d&page=16679&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d&page=16679&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16679.Q46a70873c456d-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
Line 251: Line 432:
{{BacktoTop}}
{{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:ttd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

ttdB

Mnemonic

Tartrate dehydratase

Synonyms

ECK3052, b3062, JW3034, ygjB[1], ygjB

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

69.09 minutes 

MG1655: 3205393..3205998
<gbrowseImage> name=NC_000913:3205393..3205998 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3140188..3140793
<gbrowseImage> name=NC_012967:3140188..3140793 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3092541..3093146
<gbrowseImage> name=NC_012759:3092541..3093146 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3206027..3206632
<gbrowseImage> name=NC_007779:3206027..3206632 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3303138..3303743
<gbrowseImage> name=NC_010473:3303138..3303743 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
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

ΔttdB (Keio:JW3034)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10318[3]

ttdB::Tn5KAN-I-SceI (FB21016)

Insertion at nt 142 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21016

contains pKD46

ΔttdB754::kan

PMID:16738554[2]

CGSC:103252


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

JW3034

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAAAAGATCCTGACAACCCC

Primer 2:CCTTTGATGTAATGGACGTGCTC

19F2

Kohara Phage

Genobase

PMID:3038334[6]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[3]

est. P1 cotransduction: 35% [7]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[3]

est. P1 cotransduction: 71% [7]
Synonyms:zgh-3075::Tn10, zgj-3075::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:EG11169

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11169

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001152

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947568

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1157

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010052

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. ↑ 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 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=ttdB:Gene&oldid=1479511"