zwf: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="A46a9d07545198"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''zwf''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''zwf''
Zwischenferment
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1853, b1852, JW1841''<ref name='LIB:Riley_2006'/>, JW1841''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14281.A46a9d07545198&page=14281&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1853, b1852, JW1841''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='136044'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9d075c0eff"  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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41.66 minutes, 41.66 minutes&nbsp;
41.66 minutes, 41.66 minutes&nbsp;
|
|
MG1655: 1934338..1932863<br />{{GBrowseFigureByCoord|1931863|1935338|ecoli|MG1655}}
MG1655: 1934338..1932863<br /><gbrowseImage>
name=NC_000913:1932863..1934338
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11221 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11221 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1931863..1935338 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1931863|1935338|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1932863..1934338&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1932863|1934338|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11221 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11221 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1914890..1913415<br /><gbrowseImage>
name=NC_012967:1913415..1914890
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1913415|1914890|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1913415|1914890|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1824922..1826397<br /><gbrowseImage>
name=NC_012759:1824922..1826397
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1824922|1826397|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1824922|1826397|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1938028..1936553<br />{{GBrowseFigureByCoord|1935553|1939028|ecoli_W3110|W3110}}  
W3110: 1938028..1936553<br /><gbrowseImage>
name=NC_007779:1936553..1938028
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1935553|1939028|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1936553|1938028|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2024909..2023434<br /><gbrowseImage>
name=NC_010473:2023434..2024909
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1935553..1939028 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2020484|2027859|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1936553..1938028&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2020484|2027859|FASTA Dump}}
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|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14281.O46a9d075c0eff&page=14281&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14281.O46a9d075c0eff&page=14281&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
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===Notes===
===Notes===
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|- {{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' {{Prettytable}} id='136046'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9d076b8239"  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!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;zwf (Keio:JW1841)
&Delta;zwf (Keio:JW1841)
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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=107818 CGSC9537]<ref name='LIB:cgsc'/>  
|
|-
|
zwfS100N
|
 
|
S100N
|
 
|
(in strain: ECOR 4 and ECOR 10)
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P0AC53 UniProt:P0AC53]
|-
|
''zwf-2''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:8795|CGSC:8795]]
|
|
   
   
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''zwf-1''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:19664|CGSC:19664]]
|
|-
|
''&#916;zwf-777::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:106122|CGSC:106122]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14281.N4e04cd3af33b1-->
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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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JW1841
JW1841
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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:CCtTCAAACTCATTCCAGGAACG  
Primer 2:CCtTCAAACTCATTCCAGGAACG  
|-
|-  
|
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[[eda:Gene|eda-51::Tn10]]
[[eda:Gene|eda-51::Tn10]]
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|
|
est. P1 cotransduction: 91% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 91% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
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[[uvrC:Gene|uvrC279::Tn10]]
[[uvrC:Gene|uvrC279::Tn10]]
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|
|
est. P1 cotransduction: 5% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 5% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11221 EcoCyc:EG11221] 
EcoCyc:EG11221
|
|
''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=EB1203 EchoBASE:EB1203] 
EcoGene:EG11221
|
|
''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=b1852 EcoliGenExpDB:b1852] 
RegulonDB:ECK120001199
|
|
''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=C2265 ECOL199310CYC:C2265]
[http://www.ncbi.nlm.nih.gov/gene?term=946370 GeneID:946370]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11221 EcoGene:EG11221] 
EchoBASE:EB1203
|
|
''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=ZWF ECOO157CYC:ZWF] 
ASAP:ABE-0006171
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14281.P46a9d0780867d&page=14281&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/2 CGSC:2]
|
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===Notes===
===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===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:zwf genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 19 September 2013

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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

zwf

Mnemonic

Zwischenferment

Synonyms

ECK1853, b1852, JW1841[1], JW1841

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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

41.66 minutes, 41.66 minutes 

MG1655: 1934338..1932863
<gbrowseImage> name=NC_000913:1932863..1934338 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1914890..1913415
<gbrowseImage> name=NC_012967:1913415..1914890 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1824922..1826397
<gbrowseImage> name=NC_012759:1824922..1826397 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1938028..1936553
<gbrowseImage> name=NC_007779:1936553..1938028 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2024909..2023434
<gbrowseImage> name=NC_010473:2023434..2024909 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

Δzwf (Keio:JW1841)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9537[3]

zwfS100N

S100N

(in strain: ECOR 4 and ECOR 10)

Strain variation; seeded from UniProt:P0AC53

zwf-2

CGSC:8795

zwf-1

CGSC:19664

Δzwf-777::kan

PMID:16738554[2]

CGSC:106122


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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

JW1841

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCGGTAACGCAAACAGCCCA

Primer 2:CCtTCAAACTCATTCCAGGAACG

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[3]

est. P1 cotransduction: 91% [5]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[3]

est. P1 cotransduction: 5% [5]

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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:EG11221

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11221

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001199

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946370

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1203

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006171

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. ↑ 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
  5. ↑ 5.0 5.1 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).

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