aat:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Update TableEdit tables.
Fixing REL gene coord display.
Line 34: Line 34:


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


|-
|-
!align=left |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'/>
Line 66: Line 66:
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|  id="K46a9bae38a17a"  class=" tableEdit Gene_location_table"   
{|  id="K46a9bae38a17a"  class=" tableEdit Gene_location_table"   
|-
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-  
|-  
Line 88: Line 88:


|
|
NC_012967: 943786..944490<br />{{GBrowseFigureByCoord|943786|944490|REL606|NC_012967}}
NC_012967: 944490..943786<br />{{GBrowseFigureByCoord|943786|944490|REL606|NC_012967}}
|
|
{{GBrowseLink|REL606|NC_012967|943786|944490|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|943786|944490|GBrowse (REL606)}}
Line 135: Line 135:
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|  id="Y46a9bae434217"  class=" tableEdit Gene_sequence_features_table"   
{|  id="Y46a9bae434217"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|   id="V46a9bae4747ed"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="V46a9bae4747ed"  class=" tableEdit Gene_allele_table"   
|-
|- {{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
|-  
|-  
Line 265: Line 265:
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|  id="M46a9bae51e5d9"  class=" tableEdit Gene_resource_table"   
{|  id="M46a9bae51e5d9"  class=" tableEdit Gene_resource_table"   
|-
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 322: Line 322:
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|  id="V46a9bae5a80f1"  class=" tableEdit Gene_accessions_table"   
{|  id="V46a9bae5a80f1"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 393: Line 393:
****************************************************************************************** -->
****************************************************************************************** -->
{|  id="W46a6d83884159"  class=" tableEdit Links_table"   
{|  id="W46a6d83884159"  class=" tableEdit Links_table"   
|-
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:05, 21 January 2010

{{#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=925951..926655&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 944490..943786
gbrowse_img.php?coord=943786..944490&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 927854..927150
gbrowse_img.php?coord=927150..927854&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 980583..979879
gbrowse_img.php?coord=979879..980583&genome=ecoli_DH10B&name=DH10B&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]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 47% [7]
Synonyms: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]



<protect>

References

[back to top]


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 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=1026846"