frdB:Gene: Difference between revisions

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|{{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]]
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|{{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==
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|-
|-
!{{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''


|-
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!{{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> ||
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''ECK4149, b4153, JW4114''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<protect>
<protect>
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{| 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
|-
|-  
|
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MG1655
MG1655
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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
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&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}}
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===Notes===
===Notes===
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{| 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}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
4377809
|
Edman degradation
|
PMID:6751816<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{| 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" 
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!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
|-
|-
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Strain DH10B
|
 
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D51N
|
 
|
Nonsynonomous mutation
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PMID:18245285
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[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
|
This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
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&Delta;frdB (Keio:JW4114)
&Delta;frdB (Keio:JW4114)
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[[PMID:16738554]]<ref name=PMID:16738554/>
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'/>  
|
|-
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frdBC58S
|
 
|
C58S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
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frdBC78S
|
 
|
C78S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
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frdBC63S
|
 
|
C63S
|
 
|
Affects center 1 (2Fe-2S)
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
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frdBC66S
|
 
|
C66S
|
 
|
Affects center 1 (2Fe-2S)
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC47 UniProt:P0AC47]
|-
|
''&#916;frdB780::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100994|CGSC:100994]]
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|
   
   
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===Notes===
===Notes===


==Genetic Interactions==
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW4114
JW4114
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[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
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Primer 2:CCGCGTGGTTTCAGGGTCGCGAT  
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]]
[[cadB:Gene|cadB2231::Tn10]]
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CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
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'/>
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjd-2231::Tn10  
Synonyms:zjd-2231::Tn10  
|-
|-  
|
|
[[cycA:Gene|cycA30::Tn10]]
[[cycA:Gene|cycA30::Tn10]]
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|
|
est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/>  
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10331 EcoCyc:EG10331]
[[EcoCyc]]
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|
EcoCyc:EG10331
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0327 EchoBASE:EB0327]
[[EcoGene]]
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|
EcoGene:EG10331
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4153 EcoliGenExpDB:b4153]
[[RegulonDB]]
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|
RegulonDB:ECK120000325
|-
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5241 ECOL199310CYC:C5241]
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/gene?term=948666 GeneID:948666]
|-
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10331 EcoGene:EG10331]
[[EchoBASE]]
|
|
EchoBASE:EB0327
|-
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://BioCyc.org/ECOO157/new-image?object=FRDB ECOO157CYC:FRDB]
[[ASAP]]
|
|
ASAP:ABE-0013602
|-
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
 
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/741 CGSC:741] 
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===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

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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

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Notes

Location(s) and DNA Sequence

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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>

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Notes

Sequence Features

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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]


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Notes

Alleles and Phenotypes

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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


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Notes

Genetic Interactions

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

Genetic Resources

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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]

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Notes

Accessions in Other Databases

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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

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Notes

Links

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<protect>

References

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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

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