cusB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Data loaded by TableEdit_Loader.
Update TableEdit tables.
Line 31: Line 31:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{| id="P46a9b3c8e1d7a" class=" tableEdit Gene_nomenclature_table"


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


|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
||
||
''ECK0566, b0574, JW0563, ylcD, agrB''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0566, b0574, JW0563, ylcD, agrB''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.P46a9b3c8e1d7a&page=11709&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.P46a9b3c8e1d7a&page=11709&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.P46a9b3c8e1d7a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.P46a9b3c8e1d7a-->
Line 65: Line 65:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="O46a9b3c9659a2" 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 82: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|596702|597925|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|596702|597925|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6322 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6322 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 578382..579605<br />{{GBrowseFigureByCoord|578382|579605|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|578382|579605|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|578382|579605|FASTA Dump}}
|-  
|-  
|
|
Line 115: Line 126:
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|646848|652963|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|646848|652963|FASTA Dump}}  
|-
|
[[REL606]]
|
|
NC_012967: 578382..579605<br />{{GBrowseFigureByCoord|578382|579605|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|578382|579605|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|578382|579605|FASTA Dump}}


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.O46a9b3c9659a2&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.O46a9b3c9659a2&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.O46a9b3c9659a2-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.O46a9b3c9659a2-->
Line 145: Line 145:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="Q46a9b3ca0e276" class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|-
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.Q46a9b3ca0e276&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.Q46a9b3ca0e276&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.Q46a9b3ca0e276-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.Q46a9b3ca0e276-->
Line 167: Line 167:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{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}}
{|   id="C46a9b3ca4eafd" 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 205: Line 205:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.C46a9b3ca4eafd&page=11709&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.C46a9b3ca4eafd&page=11709&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.C46a9b3ca4eafd-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.C46a9b3ca4eafd-->
Line 223: Line 223:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="H46a9b3caeb154" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|-
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 262: Line 262:
Synonyms:zbd-601::Tn10, zbe-601::Tn10  
Synonyms:zbd-601::Tn10, zbe-601::Tn10  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.H46a9b3caeb154&page=11709&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.H46a9b3caeb154&page=11709&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.H46a9b3caeb154-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.H46a9b3caeb154-->
Line 280: Line 280:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="F46a9b3cb7f572" class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|-
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 333: Line 333:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.F46a9b3cb7f572&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.F46a9b3cb7f572&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.F46a9b3cb7f572-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.F46a9b3cb7f572-->
Line 351: Line 351:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="Q46a6d13e09505" class=" tableEdit Links_table"   
|- {{table_heading_style}}
|-
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.Q46a6d13e09505&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11709.Q46a6d13e09505&page=11709&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.Q46a6d13e09505-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11709.Q46a6d13e09505-->

Revision as of 00:28, 9 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

cusB

Mnemonic
Synonyms

ECK0566, b0574, JW0563, ylcD, agrB[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

12.86 minutes 

MG1655: 596702..597925
gbrowse_img.php?coord=596702..597925&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 578382..579605
gbrowse_img.php?coord=578382..579605&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 596702..597925
gbrowse_img.php?coord=596702..597925&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 536034..537257
gbrowse_img.php?coord=536034..537257&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

DH10B

DH10B: 649294..650517
gbrowse_img.php?coord=649294..650517&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

ΔcusB (Keio:JW0563)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8688[4]

ΔcusB783::kan

PMID:16738554[3]

CGSC:100440


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

JW0563

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAAAAAATCGCGCTTATTAT

Primer 2:CCATGCGCATGGGTAGCACTTTC

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[4]

est. P1 cotransduction: 14% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[4]

est. P1 cotransduction: 20% [6]
Synonyms: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:G6322

EchoBASE (EcoliWiki Page)

EchoBASE:EB3986

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0574

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0660

EcoGene (EcoliWiki Page)

EcoGene:EG14235

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YLCD

ASAP (EcoliWikiPage)

ASAP:ABE-0001969


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. ↑ 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. ↑ 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=cusB:Gene&oldid=975305"