aat: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
|
||
''aat''  
''aat''  
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0876, b0885, JW0868, ycaA, G8002''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0876, b0885, JW0868, ycaA, G8002''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.D46a9bae31153a&page=12329&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.D46a9bae31153a&page=12329&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.D46a9bae31153a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.D46a9bae31153a-->
{{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='130187'
{|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|925951|926655|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|925951|926655|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11112 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11112 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
Line 91: Line 93:
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|927150|927854|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|927150|927854|FASTA Dump}}  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.K46a9bae38a17a&page=12329&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.K46a9bae38a17a&page=12329&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.K46a9bae38a17a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.K46a9bae38a17a-->
{{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='130188'
{|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=421aa90e079fa326b6494f812ad13e79.12329.Y46a9bae434217&page=12329&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.Y46a9bae434217&page=12329&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.Y46a9bae434217-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.Y46a9bae434217-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 129: Line 133:
*  ** 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' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
{|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}}
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]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107180 CGSC8899]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107180 CGSC8899]<ref name='LIB:cgsc'/>  
Line 161: Line 164:
|
|
MS845 has only 50% the tryptophanase activity of parent strain.
MS845 has only 50% the tryptophanase activity of parent strain.
|
|[[PMID:137233]]<ref name=PMID:137233/>
[[PMID:137233]]<ref name=PMID:137233/>
|
|
[[cgscmutation:8542|CGSC:8542]]
[[cgscmutation:8542|CGSC:8542]]
Line 178: Line 180:
|
|


|
|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[cgscmutation:99874|CGSC:99874]]
[[cgscmutation:99874|CGSC:99874]]
Line 196: Line 197:
Cells appear as clubs,spheres, or ellipsoids. Normal rod-shaped morphology was restored by addition of D-alanine or D-glutamic
Cells appear as clubs,spheres, or ellipsoids. Normal rod-shaped morphology was restored by addition of D-alanine or D-glutamic
acid to the medium.
acid to the medium.
|
|[[PMID:137233]]<ref name=PMID:137233/>
[[PMID:137233]]<ref name=PMID:137233/>
|
|
[[cgscmutation:8542|CGSC:8542]]
[[cgscmutation:8542|CGSC:8542]]
Line 213: Line 213:
|
|
When aspartate was the sole nitrogen source, the 'aat-1' mutant strain (MS845 F'128) grew about twice as fast as its parent (doubling times of 2.3 and 4.8 h, respectively).
When aspartate was the sole nitrogen source, the 'aat-1' mutant strain (MS845 F'128) grew about twice as fast as its parent (doubling times of 2.3 and 4.8 h, respectively).
|
|[[PMID:137233]]<ref name=PMID:137233/>
[[PMID:137233]]<ref name=PMID:137233/>
|
|
[[cgscmutation:8542|CGSC:8542]]
[[cgscmutation:8542|CGSC:8542]]
Line 224: Line 223:
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.V46a9bae4747ed-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.V46a9bae4747ed-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
Line 234: Line 233:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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='130190'
{|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
|-
|-  
|
|
JW0868
JW0868
Line 248: Line 247:
|
|
[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 256: Line 254:


Primer 2:CCTTCTTGTGGTGAAAACAAGCA  
Primer 2:CCTTCTTGTGGTGAAAACAAGCA  
|-
|-  
|
|
zbh-29::Tn10
zbh-29::Tn10
Line 264: Line 262:
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbi-29::Tn10  
 
|-  
Synonyms:zbi-29::Tn10  
|-
|
|
zca-1230::Tn10
zca-1230::Tn10
Line 275: Line 271:
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 47% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 47% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbj-1230::Tn10


Synonyms:zbj-1230::Tn10
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.M46a9bae51e5d9&page=12329&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.M46a9bae51e5d9&page=12329&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.M46a9bae51e5d9-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.M46a9bae51e5d9-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 295: Line 290:
*  ** 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' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|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}}
Line 345: Line 340:
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003009&formSubmitReturn=1 ASAP:ABE-0003009]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003009&formSubmitReturn=1 ASAP:ABE-0003009]
|
|
   
   
Line 353: Line 348:
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.V46a9bae5a80f1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.V46a9bae5a80f1-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 363: Line 358:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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='97001'
{|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=421aa90e079fa326b6494f812ad13e79.12329.W46a6d83884159&page=12329&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12329.W46a6d83884159&page=12329&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.W46a6d83884159-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.12329.W46a6d83884159-->
{{Links_help}}
 


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

Revision as of 18:44, 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

aat

Mnemonic
Synonyms

ECK0876, b0885, JW0868, ycaA, G8002[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

19.96 minutes 

MG1655: 926655..925951
gbrowse_img.php?coord=924951..927655&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 927854..927150
gbrowse_img.php?coord=926150..928854&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

Δaat (Keio:JW0868)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8899[4]

aat-1

Other

MS845 has only 50% the tryptophanase activity of parent strain.

PMID:137233[5]

CGSC:8542

Δaat-784::kan

PMID:16738554[3]

CGSC:99874

aat-1

Cell Shape

Cells appear as clubs,spheres, or ellipsoids. Normal rod-shaped morphology was restored by addition of D-alanine or D-glutamic acid to the medium.

PMID:137233[5]

CGSC:8542

aat-1

Growth Phenotype

When aspartate was the sole nitrogen source, the 'aat-1' mutant strain (MS845 F'128) grew about twice as fast as its parent (doubling times of 2.3 and 4.8 h, respectively).

PMID:137233[5]

CGSC:8542


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

JW0868

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCGCCTGGTTCAGCTTTCTCG

Primer 2:CCTTCTTGTGGTGAAAACAAGCA

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: % [7]nnSynonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 47% [7]nnSynonyms:zbj-1230::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:EG11112

EchoBASE (EcoliWiki Page)

EchoBASE:EB1103

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0885

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1022

EcoGene (EcoliWiki Page)

EcoGene:EG11112

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:AAT

ASAP (EcoliWikiPage)

ASAP:ABE-0003009


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. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 5.2 Deutch, CE et al. (1977) Pleiotropic phenotype of an Escherichia coli mutant lacking leucyl-, phenylalanyl-transfer ribonucleic acid-protein transferase. J. Bacteriol. 129 544-6 PubMed
  6. ↑ 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
  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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=aat:Gene&oldid=643922"