trxA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Data loaded by TableEdit_Loader.
touch
 
(39 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 27: Line 29:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|   id="N46a9fec0da414"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''trxA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''trxA''
Thioredoxin
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3773, b3781, JW5856, fipA, tsnC, dasC''<ref name='LIB:Riley_2006'/>, dasC''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec0da414&page=18121&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK3773, b3781, JW5856, fipA, tsnC, dasC''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec0da414&page=18121&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec0da414-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec0da414-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 59: Line 63:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' {{Prettytable}} id='147567'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9fec168863"  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 72: Line 76:
85.43 minutes, 85.43 minutes&nbsp;
85.43 minutes, 85.43 minutes&nbsp;
|
|
MG1655: 3963784..3964113<br />{{GBrowseFigureByCoord|3962784|3965113|ecoli|MG1655}}
MG1655: 3963784..3964113<br /><gbrowseImage>
name=NC_000913:3963784..3964113
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11031 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11031 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3962784..3965113 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3962784|3965113|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3963784..3964113&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3963784|3964113|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11031 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11031 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3927561..3927890<br /><gbrowseImage>
name=NC_012967:3927561..3927890
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3927561|3927890|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3927561|3927890|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3853453..3853782<br /><gbrowseImage>
name=NC_012759:3853453..3853782
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3853453|3853782|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3853453|3853782|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 86: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 3670920..3670591<br />{{GBrowseFigureByCoord|3669591|3671920|ecoli_W3110|W3110}}  
W3110: 3670920..3670591<br /><gbrowseImage>
name=NC_007779:3670591..3670920
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3669591|3671920|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3670591|3670920|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 4062704..4063033<br /><gbrowseImage>
name=NC_010473:4062704..4063033
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3669591..3671920 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4062046|4063691|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3670591..3670920&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4062046|4063691|FASTA Dump}}
|-class='sortbottom'
 
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.Z46a9fec168863&page=18121&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.Z46a9fec168863&page=18121&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.Z46a9fec168863-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.Z46a9fec168863-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 105: Line 168:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='147568'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9fec22d042"  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}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.H46a9fec22d042&page=18121&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
3963787
|
Edman degradation
|
PMID:4883076<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.H46a9fec22d042&page=18121&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.H46a9fec22d042-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.H46a9fec22d042-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 129: Line 206:
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46a9fec2776b4"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
Line 145: Line 222:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
Line 162: Line 239:


|
|
[[PMID:337124]]<ref name=PMID:337124/> [[PMID:3881756]]<ref name=PMID:3881756/>
PMID:337124 PMID:3881756
|
|
[[cgscmutation:5031|CGSC:5031]]
[[cgscmutation:5031|CGSC:5031]]
|
|
amber (UAG) mutation  
amber (UAG) mutation  
|-
|
''&#916;trxA307''
|
|
|
|
|
|
[[cgscmutation:10957|CGSC:10957]]
|
|-
|
''trxA11''(ts)
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec2776b4&page=18121&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
 
|
 
|
temperature sensitive
|
PMID:3881756
|
[[cgscmutation:88597|CGSC:88597]]
|
|-
|
trxA
|
deletion
|
 
|
Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec2776b4&page=18121&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec2776b4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.N46a9fec2776b4-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18121.A4e04c4ffa03a7-->
<!--
******************************************************************************************
*
*  ** 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="A4e04c4ffa03a7"  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.18121.A4e04c4ffa03a7&page=18121&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18121.A4e04c4ffa03a7--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 182: Line 332:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' {{Prettytable}} id='147570'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9fec33befe"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW5856
JW5856
Line 197: Line 347:
[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 204: Line 354:


Primer 2:CCtGCCAGGTTAGCGTCGAGGAA  
Primer 2:CCtGCCAGGTTAGCGTCGAGGAA  
|-
|-
|
[[:Category:Kohara_Phage:7B1|7B1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=555 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2A8|2A8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=556 Genobase]
|
PMID:3038334
|-  
|
|
[[ilvD:Gene|ilvD500::Tn10]]
[[ilvD:Gene|ilvD500::Tn10]]
Line 212: Line 380:
CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:ilv500::Tn10  
Synonyms:ilv500::Tn10  
|-
|-  
|
|
metEo-3079::Tn10
metEo-3079::Tn10
Line 223: Line 390:
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.


Synonyms:metE3079::Tn10
|- class="tableEdit_footer"
 
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.S46a9fec33befe&page=18121&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
 
The Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.S46a9fec33befe&page=18121&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.S46a9fec33befe-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.S46a9fec33befe-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 243: Line 407:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' {{Prettytable}} id='147571'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9fec3db93d"  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=EG11031 EcoCyc:EG11031] 
EcoCyc:EG11031
|
|
''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=EB1024 EchoBASE:EB1024] 
EcoGene:EG11031
|
|
''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=b3781 EcoliGenExpDB:b3781] 
RegulonDB:ECK120001020
|
|
''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=C4701 ECOL199310CYC:C4701]
[http://www.ncbi.nlm.nih.gov/gene?term=948289 GeneID:948289]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11031 EcoGene:EG11031] 
EchoBASE:EB1024
|
|
''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=TRXA ECOO157CYC:TRXA] 
ASAP:ABE-0012357
|
|
''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=421aa90e079fa326b6494f812ad13e79.18121.F46a9fec3db93d&page=18121&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/65 CGSC:65] 
|
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.F46a9fec3db93d&page=18121&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.F46a9fec3db93d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.F46a9fec3db93d-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 313: Line 471:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='99887'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a718c61760e"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
|-class='sortbottom'
 
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.P46a718c61760e&page=18121&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18121.P46a718c61760e&page=18121&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.P46a718c61760e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18121.P46a718c61760e-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
Line 330: Line 489:
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
Line 338: Line 496:
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:trx genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:49, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

trxA

Mnemonic

Thioredoxin

Synonyms

ECK3773, b3781, JW5856, fipA, tsnC, dasC[1], dasC

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

85.43 minutes, 85.43 minutes 

MG1655: 3963784..3964113
<gbrowseImage> name=NC_000913:3963784..3964113 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3927561..3927890
<gbrowseImage> name=NC_012967:3927561..3927890 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3853453..3853782
<gbrowseImage> name=NC_012759:3853453..3853782 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3670920..3670591
<gbrowseImage> name=NC_007779:3670591..3670920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4062704..4063033
<gbrowseImage> name=NC_010473:4062704..4063033 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

3963787

Edman degradation

PMID:4883076[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

ΔtrxA (Keio:JW5856)

deletion

deletion

PMID:16738554[3]

Shigen

trxA1(Am)

PMID:337124[4] PMID:3881756[5]

CGSC:5031

amber (UAG) mutation

ΔtrxA307

CGSC:10957

trxA11(ts)

temperature sensitive

PMID:3881756[5]

CGSC:88597

trxA

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[6]

fig 2

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

JW5856

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAGCGATAAAATTATTCACCT

Primer 2:CCtGCCAGGTTAGCGTCGAGGAA

7B1

Kohara Phage

Genobase

PMID:3038334[8]

2A8

Kohara Phage

Genobase

PMID:3038334[8]

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[9]

est. P1 cotransduction: 69% [10]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[9]

est. P1 cotransduction: 14% [10]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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:EG11031

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11031

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001020

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948289

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012357

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. ↑ Holmgren, A (1968) Thioredoxin. 6. The amino acid sequence of the protein from escherichia coli B. Eur. J. Biochem. 6 475-84 PubMed
  3. ↑ 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. ↑ Mark, DF et al. (1977) Genetic mapping of trxA, a gene affecting thioredoxin in Escherichia coli K12. Mol. Gen. Genet. 155 145-52 PubMed
  5. ↑ 5.0 5.1 Russel, M & Model, P (1985) Thioredoxin is required for filamentous phage assembly. Proc. Natl. Acad. Sci. U.S.A. 82 29-33 PubMed
  6. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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=trxA:Gene&oldid=1480231"