frdB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
imported>WikiEntryBot
Automated import of articles
 
touch
 
(50 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|frdB}}{{Tab On|Gene|frdB}}{{Tab|Gene Product(s)|frdB}}{{Tab|Expression|frdB}}{{Tab|Evolution|frdB}}{{Tab|On One Page|frdB}}{{TabsBottom}}
{{Tab|Quickview|frdB}}{{Tab On|Gene|frdB}}{{Tab|Gene Product(s)|frdB}}{{Tab|Expression|frdB}}{{Tab|Evolution|frdB}}{{Tab|On One Page|frdB}}{{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..O469fb4372d012-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.A46aa0881e1f3f-->
{|{{Prettytable}}
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|  id="A46aa0881e1f3f"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''frdB''  
''frdB''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Fumarate reductase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4149, b4153, JW4114''<ref name='LIB:Riley_2006'/>, JW4114''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.A46aa0881e1f3f&page=18871&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK4149, b4153, JW4114''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..O469fb4372d012&page=&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..O469fb4372d012-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.A46aa0881e1f3f-->
{{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..L469fb43779546-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.P46aa088271085-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='29398'
******************************************************************************************
*
*  ** 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="P46aa088271085"  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:
94.36 minutes, 94.36 minutes&nbsp;
94.36 minutes, 94.36 minutes&nbsp;
|
|
MG1655: 4378540..4377806<br />{{GBrowseFigureByCoord|4376806|4379540|ecoli|MG1655}}
MG1655: 4378540..4377806<br /><gbrowseImage>
name=NC_000913:4377806..4378540
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10331 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10331 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4376806..4379540 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4376806|4379540|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4377806..4378540&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4377806|4378540|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10331 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10331 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4359228..4358494<br /><gbrowseImage>
name=NC_012967:4358494..4359228
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4358494|4359228|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4358494|4359228|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 4316541..4317275<br /><gbrowseImage>
name=NC_012759:4316541..4317275
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4316541|4317275|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4316541|4317275|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 66: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 4385197..4384463<br />{{GBrowseFigureByCoord|4383463|4386197|ecoli_W3110|W3110}}
W3110: 4385197..4384463<br /><gbrowseImage>
name=NC_007779:4384463..4385197
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4383463..4386197 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4383463|4386197|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4384463..4385197&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4384463|4385197|FASTA Dump}}
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..L469fb43779546&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.P46aa088271085&page=18871&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..L469fb43779546-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.P46aa088271085-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 81: Line 148:


==Sequence Features==
==Sequence Features==
<!--box uid=421aa90e079fa326b6494f812ad13e79..P469fb437a235b-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.W46aa088339874-->
{|class = 'sortable' {{Prettytable}} id='29399'
<!--
******************************************************************************************
*
*  ** 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="W46aa088339874"  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..P469fb437a235b&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4377809
|
Edman degradation
|
PMID:6751816<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.W46aa088339874&page=18871&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..P469fb437a235b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.W46aa088339874-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 96: Line 183:


==Alleles and Phenotypes==
==Alleles and Phenotypes==
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469fb437b2447-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.M46aa088385244-->
{|class = 'sortable' {{Prettytable}} id='29400'
<!--
******************************************************************************************
*
*  ** 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="M46aa088385244"  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..V469fb437b2447&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|
Strain DH10B
|
 
|
D51N
|
 
|
Nonsynonomous mutation
|
PMID:18245285
|
[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
|
This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
|-
|
&Delta;frdB (Keio:JW4114)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109244 CGSC10963]<ref name='LIB:cgsc'/>
|
|-
|
frdBC58S
|
 
|
C58S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
|
frdBC78S
|
 
|
C78S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
|
frdBC63S
|
 
|
C63S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
|
frdBC66S
|
 
|
C66S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
|
''&#916;frdB780::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100994|CGSC:100994]]
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.M46aa088385244&page=18871&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469fb437b2447-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.M46aa088385244-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18871.O4e04bb65d2ddf-->
<!--
******************************************************************************************
*
*  ** 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="O4e04bb65d2ddf"  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.18871.O4e04bb65d2ddf&page=18871&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18871.O4e04bb65d2ddf--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
<!--box uid=421aa90e079fa326b6494f812ad13e79..O469fb437c253f-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.T46aa08844ca9e-->
{|class = 'sortable' {{Prettytable}} id='29401'
<!--
******************************************************************************************
*
*  ** 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="T46aa08844ca9e"  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..O469fb437c253f&page=&pagename={{FULLPAGENAMEE}} edit table] || || ||
|
JW4114
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGCTGAGATGAAAAACCTGAA
 
Primer 2:CCGCGTGGTTTCAGGGTCGCGAT
|-
|
[[:Category:Kohara_Phage:1D4|1D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=650 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3H6|3H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=651 Genobase]
|
PMID:3038334
|-
|
[[cadB:Gene|cadB2231::Tn10]]
|
Linked marker
|
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjd-2231::Tn10
|-
|
[[cycA:Gene|cycA30::Tn10]]
|
Linked marker
|
CAG12073 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40604 CGSC7482]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/>
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.T46aa08844ca9e&page=18871&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..O469fb437c253f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.T46aa08844ca9e-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 126: Line 420:


==Accessions in Other Databases==
==Accessions in Other Databases==
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469fb437d26a4-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.R46aa0884ef2bf-->
{|class = 'sortable' {{Prettytable}} id='29402'
<!--
******************************************************************************************
*
*  ** 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="R46aa0884ef2bf"  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=EG10331 EcoCyc:EG10331] 
EcoCyc:EG10331
|
|
''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=EB0327 EchoBASE:EB0327] 
EcoGene:EG10331
|
|
''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=b4153 EcoliGenExpDB:b4153] 
RegulonDB:ECK120000325
|
|
''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=C5241 ECOL199310CYC:C5241]
[http://www.ncbi.nlm.nih.gov/gene?term=948666 GeneID:948666]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10331 EcoGene:EG10331] 
EchoBASE:EB0327
|
|
''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=FRDB ECOO157CYC:FRDB] 
ASAP:ABE-0013602
|
|
''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=421aa90e079fa326b6494f812ad13e79.18871.R46aa0884ef2bf&page=18871&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/741 CGSC:741] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..G469fb437d26a4&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469fb437d26a4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.R46aa0884ef2bf-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 190: Line 484:


==Links==
==Links==
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.V46a7216d8fb43-->
<!--
******************************************************************************************
*
*  ** 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="V46a7216d8fb43"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
!|Name!!URL!!Comments
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18871.V46a7216d8fb43&page=18871&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18871.V46a7216d8fb43-->




<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:frd genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

frdB

Mnemonic

Fumarate reductase

Synonyms

ECK4149, b4153, JW4114[1], JW4114

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

94.36 minutes, 94.36 minutes 

MG1655: 4378540..4377806
<gbrowseImage> name=NC_000913:4377806..4378540 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4359228..4358494
<gbrowseImage> name=NC_012967:4358494..4359228 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4316541..4317275
<gbrowseImage> name=NC_012759:4316541..4317275 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4385197..4384463
<gbrowseImage> name=NC_007779:4384463..4385197 source=W3110 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

4377809

Edman degradation

PMID:6751816[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

Strain DH10B

D51N

Nonsynonomous mutation

PMID:18245285[3]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔfrdB (Keio:JW4114)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10963[5]

frdBC58S

C58S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC78S

C78S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC63S

C63S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC66S

C66S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

ΔfrdB780::kan

PMID:16738554[4]

CGSC:100994


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

JW4114

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCTGAGATGAAAAACCTGAA

Primer 2:CCGCGTGGTTTCAGGGTCGCGAT

1D4

Kohara Phage

Genobase

PMID:3038334[7]

3H6

Kohara Phage

Genobase

PMID:3038334[7]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[5]

est. P1 cotransduction: 46% [8]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[5]

est. P1 cotransduction: 11% [8]

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:EG10331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10331

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000325

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948666

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0327

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013602

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. ↑ Cole, ST et al. (1982) Location and nucleotide sequence of frdB, the gene coding for the iron-sulphur protein subunit of the fumarate reductase of Escherichia coli. Eur. J. Biochem. 126 211-6 PubMed
  3. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 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=frdB:Gene&oldid=1480605"