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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|fre}}{{Tab On|Gene|fre}}{{Tab|Gene Product(s)|fre}}{{Tab|Expression|fre}}{{Tab|Evolution|fre}}{{Tab|On One Page|fre}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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{|  id="G46aa005b24cb4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''fre''  
''fre''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Flavin reductase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, fadI, flrD''


|-
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!{{table_heading_style}} |Synonyms
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''ECK3836, b3844, JW3820, fadI, fsrC, flrd, luxG, G2019, ubiB, lux''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<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="N46aa005ba7af0"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!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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86.74 minutes&nbsp;
86.74 minutes&nbsp;
|
|
MG1655: 4024550..4025251<br />{{GBrowseFigureByCoord|4023550|4026251|ecoli|MG1655}}
MG1655: 4024550..4025251<br /><gbrowseImage>
name=NC_000913:4024550..4025251
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10334 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10334 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4023550..4026251 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4023550|4026251|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4024550..4025251&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4024550|4025251|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10334 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10334 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 4004998..4005699<br /><gbrowseImage>
name=NC_012967:4004998..4005699
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4004998|4005699|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4004998|4005699|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3914219..3914920<br /><gbrowseImage>
name=NC_012759:3914219..3914920
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3914219|3914920|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3914219|3914920|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 3610154..3609453<br />{{GBrowseFigureByCoord|3608453|3611154|ecoli_W3110|W3110}}
W3110: 3610154..3609453<br /><gbrowseImage>
name=NC_007779:3609453..3610154
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3608453..3611154 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3608453|3611154|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3609453..3610154&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3609453|3610154|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 4123470..4124171<br /><gbrowseImage>
name=NC_010473:4123470..4124171
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4122068|4125573|GBrowse(DH10B)}}
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{{GBrowseFastaLink|DH10B|NC_010473|4122068|4125573|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aa005c6d02b"  class=" tableEdit Gene_sequence_features_table" 
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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]]
|
4024553
|
Edman degradation
|
PMID:2050627<br />
|
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46aa005cb77ac"  class=" tableEdit Gene_allele_table dataTable" 
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!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'
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''fre(del)'' (Keio:JW3820)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=109044 CGSC10763]<ref name='LIB:cgsc'/>
|
|-
|
''fre-352''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:5420|CGSC:5420]]
|
|-
|
''fre-784(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101000|CGSC:101000]]
|
|-
|
''fre784(del)''::FRTKanFRT
|
 
|
 
|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
 
Experimental Strain: SMR12007
|
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
|-
|
SMR4562 yiaG-yfp FRTcatFRT ''fre784(del)''::FRTKanFRT
|
Deletion & Insertion
|
 
|
Sigma <sup>S</sup> activity
|
Decrease in Sigma <sup>S</sup> activity
 
 
 
|
PMID:23224554
|
Parental Strain: SMR10582
Experimental Strain: SMR14267
|
See table S8 for full experimental results. 
|-
|
CAG45114 ''fre784(del)''::FRTKanFRT
|
deletion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15362
|
See table S11 for experimental results. 
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04bb6cd9110"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|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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JW3820
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCACAACCTTAAGCTGTAAAGT
 
Primer 2:CCGATAAATGCAAACGCATCGCC
|-
|
[[:Category:Kohara_Phage:16G1|16G1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=550 Genobase]
|
PMID:3038334
|-
|
metEo-3079::Tn10
|
Linked marker
|
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 57% <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.
|-
|
[[fadA:Gene|fad-751::Tn10]]
|
Linked marker
|
CAG18496 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40344 CGSC7465]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 92% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:fadAB101::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{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=EG10334 EcoCyc:EG10334] 
EcoCyc:EG10334
|
|
''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=EB0330 EchoBASE:EB0330] 
EcoGene:EG10334
|
|
''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=b3844 EcoliGenExpDB:b3844] 
RegulonDB:ECK120000328
|
|
''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=C4791 ECOL199310CYC:C4791]
[http://www.ncbi.nlm.nih.gov/gene?term=948325 GeneID:948325]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10334 EcoGene:EG10334] 
EchoBASE:EB0330
|
|
''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=UBIB ECOO157CYC:UBIB] 
ASAP:ABE-0012559
|
|
''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=421aa90e079fa326b6494f812ad13e79.18247.N46aa005e29b12&page=18247&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/49 CGSC:49] 
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===Notes===
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==Links==
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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:fre genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 19 September 2013

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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

fre

Mnemonic

Flavin reductase

Synonyms

ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux[1][2], fadI, flrD

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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

86.74 minutes 

MG1655: 4024550..4025251
<gbrowseImage> name=NC_000913:4024550..4025251 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4004998..4005699
<gbrowseImage> name=NC_012967:4004998..4005699 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3914219..3914920
<gbrowseImage> name=NC_012759:3914219..3914920 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3610154..3609453
<gbrowseImage> name=NC_007779:3609453..3610154 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4123470..4124171
<gbrowseImage> name=NC_010473:4123470..4124171 source=DH10B 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

4024553

Edman degradation

PMID:2050627[3]


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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

fre(del) (Keio:JW3820)

deletion

deletion

PMID:16738554[4]

Shigen

CGSC10763[5]

fre-352

CGSC:5420

fre-784(del)::kan

PMID:16738554[4]

CGSC:101000

fre784(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[6]

Parental Strain: SMR4562

Experimental Strain: SMR12007

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

SMR4562 yiaG-yfp FRTcatFRT fre784(del)::FRTKanFRT

Deletion & Insertion

Sigma S activity

Decrease in Sigma S activity


PMID:23224554[6]

Parental Strain: SMR10582 Experimental Strain: SMR14267

See table S8 for full experimental results.

CAG45114 fre784(del)::FRTKanFRT

deletion

SigmaE activity

Decrease in sigmaE activity

PMID:23224554[6]

Parental Strain: CAG45114 Experimental Strain: SMR15362

See table S11 for experimental results.

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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

JW3820

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACAACCTTAAGCTGTAAAGT

Primer 2:CCGATAAATGCAAACGCATCGCC

16G1

Kohara Phage

Genobase

PMID:3038334[8]

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 57% [9]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[5]

est. P1 cotransduction: 92% [9]
Synonyms:fadAB101::Tn10

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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:EG10334

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10334

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000328

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948325

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0330

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012559

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Spyrou, G et al. (1991) Characterization of the flavin reductase gene (fre) of Escherichia coli and construction of a plasmid for overproduction of the enzyme. J. Bacteriol. 173 3673-9 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. ↑ 6.0 6.1 6.2 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  7. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  8. ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  9. ↑ 9.0 9.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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