fepC: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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{|{{Prettytable}}
{|   id="E46a9b41b3ce93"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''fepC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''fepC''
Ferrienterobactin permease
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0581, b0588, JW0580''<ref name='LIB:Riley_2006'/>, JW0580''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11739.E46a9b41b3ce93&page=11739&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0581, b0588, JW0580''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128417'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9b41bb47e2"  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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13.33 minutes&nbsp;
13.33 minutes&nbsp;
|
|
MG1655: 619422..618607<br />{{GBrowseFigureByCoord|617607|620422|ecoli|MG1655}}
MG1655: 619422..618607<br /><gbrowseImage>
name=NC_000913:618607..619422
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10295 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10295 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:617607..620422 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|617607|620422|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:618607..619422&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|618607|619422|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10295 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10295 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 602907..602092<br /><gbrowseImage>
name=NC_012967:602092..602907
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|602092|602907|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|602092|602907|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 521367..522182<br /><gbrowseImage>
name=NC_012759:521367..522182
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|521367|522182|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|521367|522182|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 619422..618607<br />{{GBrowseFigureByCoord|617607|620422|ecoli_W3110|W3110}}  
W3110: 619422..618607<br /><gbrowseImage>
name=NC_007779:618607..619422
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|617607|620422|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|618607|619422|FASTA Dump}}
|-
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[[DH10B]]
|
 
|
DH10B: 558754..557939<br /><gbrowseImage>
name=NC_010473:557939..558754
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|556309|560384|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|556309|560384|FASTA Dump}}
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:617607..620422 GBrowse(W3110)]
DH10B: 672014..671199<br /><gbrowseImage>
name=NC_010473:671199..672014
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:618607..619422&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|669569|673644|GBrowse(DH10B)}}
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{{GBrowseFastaLink|DH10B|NC_010473|669569|673644|FASTA Dump}}
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128418'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9b41c5db4a"  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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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|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="S46a9b41c9db3e"  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
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|
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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=106980 CGSC8699]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106980 CGSC8699]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0002025 fepC::Tn5KAN-2] (FB20206)
|
Insertion at nt 727 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20206]
|
does not contain [[pKD46]]
|-  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100840|CGSC:100840]]
[[cgscmutation:100840|CGSC:100840]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11739.S46a9b41c9db3e&page=11739&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11739.I4e04bae4f1a8b-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I4e04bae4f1a8b"  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.11739.I4e04bae4f1a8b&page=11739&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW0580
JW0580
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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:CCACTATTTGCGGTTGAAGGTGC  
Primer 2:CCACTATTTGCGGTTGAAGGTGC  
|-
|-
|
[[:Category:Kohara_Phage:2D12|2D12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=164 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:25A7|25A7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=165 Genobase]
|
PMID:3038334
|-  
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|
[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  
|-
|-  
|
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[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
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CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbd-601::Tn10, zbe-601::Tn10


Synonyms:zbd-601::Tn10, zbe-601::Tn10
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===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="U46a9b41dcf716"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10295 EcoCyc:EG10295]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0291 EchoBASE:EB0291]
EcoCyc:EG10295
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0588 EcoliGenExpDB:b0588]
EcoGene:EG10295
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0675 ECOL199310CYC:C0675]
RegulonDB:ECK120000289
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10295 EcoGene:EG10295]
[http://www.ncbi.nlm.nih.gov/gene?term=945201 GeneID:945201]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=FEPC ECOO157CYC:FEPC]
EchoBASE:EB0291
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/4987 CGSC:4987]
ASAP:ABE-0002025
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0002025&formSubmitReturn=1 ASAP:ABE-0002025] 
|


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[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:fep genes]]
[[Category:fep genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

fepC

Mnemonic

Ferrienterobactin permease

Synonyms

ECK0581, b0588, JW0580[1], JW0580

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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

13.33 minutes 

MG1655: 619422..618607
<gbrowseImage> name=NC_000913:618607..619422 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 602907..602092
<gbrowseImage> name=NC_012967:602092..602907 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 521367..522182
<gbrowseImage> name=NC_012759:521367..522182 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 619422..618607
<gbrowseImage> name=NC_007779:618607..619422 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 558754..557939
<gbrowseImage> name=NC_010473:557939..558754 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 672014..671199
<gbrowseImage> name=NC_010473:671199..672014 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
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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

ΔfepC (Keio:JW0580)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8699[3]

fepC::Tn5KAN-2 (FB20206)

Insertion at nt 727 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20206

does not contain pKD46

ΔfepC726::kan

PMID:16738554[2]

CGSC:100840


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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

JW0580

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACCGAATCAGTAGCCCGTTT

Primer 2:CCACTATTTGCGGTTGAAGGTGC

2D12

Kohara Phage

Genobase

PMID:3038334[6]

25A7

Kohara Phage

Genobase

PMID:3038334[6]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 2% [7]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 54% [7]
Synonyms:zbd-601::Tn10, zbe-601::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:EG10295

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10295

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000289

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945201

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0291

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002025

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. ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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