eutD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|eutD}}{{Tab On|Gene|eutD}}{{Tab|Gene Product(s)|eutD}}{{Tab|Expression|eutD}}{{Tab|Evolution|eutD}}{{Tab|On One Page|eutD}}{{TabsBottom}}
{{Tab|Quickview|eutD}}{{Tab On|Gene|eutD}}{{Tab|Gene Product(s)|eutD}}{{Tab|Expression|eutD}}{{Tab|Evolution|eutD}}{{Tab|On One Page|eutD}}{{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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{{BacktoTop}}
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{|   id="A46a9de7584bcf"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''eutD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''eutD''
Ethanolamine utilization
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''eutI, ECK2453, b2458, JW2442, ypfA''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, ypfA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15481.A46a9de7584bcf&page=15481&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''eutI, ECK2453, b2458, JW2442, ypfA''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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{{Gene_nomenclature_help}}
 
<!--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="B46a9de760ed12"  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
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55.4 minutes&nbsp;
55.4 minutes&nbsp;
|
|
MG1655: 2571527..2570511<br />{{GBrowseFigureByCoord|2569511|2572527|ecoli|MG1655}}
MG1655: 2571527..2570511<br /><gbrowseImage>
name=NC_000913:2570511..2571527
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7288 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7288 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2569511..2572527 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2569511|2572527|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2570511..2571527&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2570511|2571527|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7288 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7288 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2493318..2494334<br /><gbrowseImage>
name=NC_012967:2493318..2494334
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2493318|2494334|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2493318|2494334|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2456316..2457332<br /><gbrowseImage>
name=NC_012759:2456316..2457332
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2456316|2457332|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2456316|2457332|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2572161..2571145<br />{{GBrowseFigureByCoord|2570145|2573161|ecoli_W3110|W3110}}
W3110: 2572161..2571145<br /><gbrowseImage>
name=NC_007779:2571145..2572161
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2570145..2573161 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2570145|2573161|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2571145..2572161&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2571145|2572161|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="B46a9de76bb3ea"  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
|-class='sortbottom'
 
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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="V46a9de770ce13"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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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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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008097 eutI::Tn5KAN-I-SceI] (FB20811)
|
Insertion at nt 542 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20811]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008097 eutI::Tn5KAN-I-SceI] (FB20812)
|
Insertion at nt 542 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20812]
|
contains [[pKD46]]
|-
|
''&#916;eutD778::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:106170|CGSC:106170]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9de77b98ba"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:4E10|4E10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=421 Genobase]
|
PMID:3038334
 
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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}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7288 EcoCyc:G7288] 
EcoCyc:G7288
|
|
''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=EB3940 EchoBASE:EB3940] 
EcoGene:EG14188
|
|
''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=b2458 EcoliGenExpDB:b2458] 
RegulonDB:ECK120003862
|
|
''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=C2983 ECOL199310CYC:C2983]
[http://www.ncbi.nlm.nih.gov/gene?term=946940 GeneID:946940]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14188 EcoGene:EG14188] 
EchoBASE:EB3940
|
|
''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=EUTI ECOO157CYC:EUTI] 
ASAP:ABE-0008097
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<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 not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:eut genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

eutD

Mnemonic

Ethanolamine utilization

Synonyms

eutI, ECK2453, b2458, JW2442, ypfA[1][2], ypfA

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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

55.4 minutes 

MG1655: 2571527..2570511
<gbrowseImage> name=NC_000913:2570511..2571527 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2493318..2494334
<gbrowseImage> name=NC_012967:2493318..2494334 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2456316..2457332
<gbrowseImage> name=NC_012759:2456316..2457332 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2572161..2571145
<gbrowseImage> name=NC_007779:2571145..2572161 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
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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

eutI::Tn5KAN-I-SceI (FB20811)

Insertion at nt 542 in Minus orientation

PMID:15262929[3]

E. coli Genome Project:FB20811

does not contain pKD46

eutI::Tn5KAN-I-SceI (FB20812)

Insertion at nt 542 in Minus orientation

PMID:15262929[3]

E. coli Genome Project:FB20812

contains pKD46

ΔeutD778::kan

PMID:16738554[4]

CGSC:106170


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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

4E10

Kohara Phage

Genobase

PMID:3038334[6]

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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:G7288

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14188

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003862

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946940

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3940

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008097

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. ↑ 3.0 3.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ 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. ↑ 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. ↑ 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

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