tfaD:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
imported>Wikientrybot
No edit summary
Line 27: Line 27:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''tfaD''  
''tfaD''  
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0553, b0561, JW5815, yicF, ybcX, ylcF''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0553, b0561, JW5815, yicF, ybcX, ylcF''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.Y46a9b37fe3f0e&page=11683&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.Y46a9b37fe3f0e&page=11683&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.Y46a9b37fe3f0e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.Y46a9b37fe3f0e-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 59: Line 61:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' {{Prettytable}} id='128249'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{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
Line 80: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|580757|581320|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|580757|581320|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6315 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6315 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
Line 91: Line 93:
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|580757|581320|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|580757|581320|FASTA Dump}}  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.O46a9b38068512&page=11683&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.O46a9b38068512&page=11683&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.O46a9b38068512-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.O46a9b38068512-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 105: Line 108:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='128250'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature type!!Location!!Description
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.G46a9b38113cfb&page=11683&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.G46a9b38113cfb&page=11683&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.G46a9b38113cfb-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.G46a9b38113cfb-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 126: Line 130:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' {{Prettytable}} id='128251'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
|- {{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
|-
|-  
|
|
&Delta;tfaD (Keio:JW5815)
&Delta;tfaD (Keio:JW5815)
Line 144: Line 148:
|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.W46a9b38153d38&page=11683&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.W46a9b38153d38&page=11683&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.W46a9b38153d38-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.W46a9b38153d38-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
Line 164: Line 168:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' {{Prettytable}} id='128252'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW5815
JW5815
Line 178: Line 182:
|
|
[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]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
Line 186: Line 189:


Primer 2:CCtTCCCTGACAGGGTTCGTAGG  
Primer 2:CCtTCCCTGACAGGGTTCGTAGG  
|-
|-  
|
|
[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
Line 194: Line 197:
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: 33% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 33% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:purE79::Tn10  
 
|-  
Synonyms:purE79::Tn10  
|-
|
|
[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
Line 205: Line 206:
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: 7% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbd-601::Tn10, zbe-601::Tn10


Synonyms:zbd-601::Tn10, zbe-601::Tn10
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.I46a9b381f0256&page=11683&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.I46a9b381f0256&page=11683&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.I46a9b381f0256-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.I46a9b381f0256-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 222: Line 222:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' {{Prettytable}} id='128253'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6315 EcoCyc:G6315]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6315 EcoCyc:G6315]
|
|
   
   
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3404 EchoBASE:EB3404]
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3404 EchoBASE:EB3404]
|
|
   
   
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0561 EcoliGenExpDB:b0561]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0561 EcoliGenExpDB:b0561]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3173 ECOL199310CYC:C3173]
[http://BioCyc.org/ECOL199310/new-image?object=C3173 ECOL199310CYC:C3173]
|
|
   
   
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13640 EcoGene:EG13640]
[http://ecogene.org/geneinfo.php?eg_id=EG13640 EcoGene:EG13640]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z2983 ECOO157CYC:Z2983]
[http://BioCyc.org/ECOO157/new-image?object=Z2983 ECOO157CYC:Z2983]
|
|
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.Z46a9b382846b3&page=11683&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.Z46a9b382846b3&page=11683&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.Z46a9b382846b3-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.Z46a9b382846b3-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 285: Line 286:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='96678'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.H46a6d0f22905a&page=11683&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11683.H46a6d0f22905a&page=11683&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.H46a6d0f22905a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11683.H46a6d0f22905a-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 18:45, 21 January 2009

{{#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 Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

tfaD

Mnemonic
Synonyms

ECK0553, b0561, JW5815, yicF, ybcX, ylcF[1][2]

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

12.52 minutes 

MG1655: 580757..581320
gbrowse_img.php?coord=579757..582320&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 580757..581320
gbrowse_img.php?coord=579757..582320&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit table


Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature type Location Description
edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔtfaD (Keio:JW5815)

deletion

deletion

PMID:16738554[3]

Shigen


edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5815

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAATGCGATGGGCAGCGACTA

Primer 2:CCtTCCCTGACAGGGTTCGTAGG

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[5]

est. P1 cotransduction: 33% [6]nnSynonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: 7% [6]nnSynonyms:zbd-601::Tn10, zbe-601::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G6315

EchoBASE (EcoliWiki Page)

EchoBASE:EB3404

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0561

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3173

EcoGene (EcoliWiki Page)

EcoGene:EG13640

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z2983


edit table


Notes

Links

[back to top]


Name URL Comments
edit table


References

[back to top]


  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. ↑ 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
  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 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=tfaD:Gene&oldid=643963"