glcB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Fixing REL gene coord display.
touch
 
(20 intermediate revisions by 2 users not shown)
Line 14: Line 14:
|{{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]]
Line 31: Line 33:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{| id="M46a9eab3ab908"  class=" tableEdit Gene_nomenclature_table"   
{|   id="M46a9eab3ab908"  class=" tableEdit Gene_nomenclature_table"   


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''glcB''  
''glcB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Glycolate
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2970, b2976, JW2943, glc''<ref name='LIB:Riley_2006'/>
''ECK2970, b2976, JW2943, glc''<ref name='LIB:Riley_2006'/>, glc''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 65: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="R46a9eab43c5fe"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9eab43c5fe"  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
Line 74: Line 76:
67.24 minutes&nbsp;
67.24 minutes&nbsp;
|
|
MG1655: 3121827..3119656<br />{{GBrowseFigureByCoord|3119656|3121827|ecoli|MG1655}}
MG1655: 3121827..3119656<br /><gbrowseImage>
name=NC_000913:3119656..3121827
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG20080 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG20080 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3118656|3122827|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3118656|3122827|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3119656|3121827|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3119656|3121827|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG20080 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG20080 EcoCyc Sequence Dump]  
|-  
|-  
Line 88: Line 95:


|
|
NC_012967: 3050697..3048526<br />{{GBrowseFigureByCoord|3048526|3050697|REL606|NC_012967}}
NC_012967: 3050697..3048526<br /><gbrowseImage>
name=NC_012967:3048526..3050697
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|3048526|3050697|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3048526|3050697|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|3048526|3050697|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|3048526|3050697|FASTA Dump}}  
|-
|
[[BW2952]]
|
|
NC_012759: 3006804..3008975<br /><gbrowseImage>
name=NC_012759:3006804..3008975
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|3006804|3008975|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3006804|3008975|FASTA Dump}}
|-  
|-  
|
|
Line 99: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 3122461..3120290<br />{{GBrowseFigureByCoord|3120290|3122461|ecoli_W3110|W3110}}
W3110: 3122461..3120290<br /><gbrowseImage>
name=NC_007779:3120290..3122461
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3119290|3123461|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3119290|3123461|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3120290|3122461|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3120290|3122461|FASTA Dump}}  
|-  
|-  
|
|
Line 110: Line 143:


|
|
DH10B: 3219572..3217401<br />{{GBrowseFigureByCoord|3217401|3219572|ecoli_DH10B|DH10B}}
DH10B: 3219572..3217401<br /><gbrowseImage>
name=NC_010473:3217401..3219572
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3213059|3223914|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3213059|3223914|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3213059|3223914|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3213059|3223914|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 134: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="Z46a9eab4edea1"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9eab4edea1"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
3119659
|
Edman degradation
|
PMID:7925370<br />
|


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16515.Z46a9eab4edea1&page=16515&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16515.Z46a9eab4edea1&page=16515&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.16515.Z46a9eab4edea1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.16515.Z46a9eab4edea1-->
Line 156: Line 207:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="Z46a9eab544a45"  class=" tableEdit Gene_allele_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z46a9eab544a45"  class=" tableEdit Gene_allele_table dataTable"   
|- {{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
Line 174: Line 225:
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108553 CGSC10272]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108553 CGSC10272]<ref name='LIB:cgsc'/>  
|
|-
|
&Delta;glcB::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Alanine]]
|
PMID:16095938
|
|
|
   
   
Line 219: Line 287:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16515.T4e04bc0447ffc-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T4e04bc0447ffc"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.16515.T4e04bc0447ffc&page=16515&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16515.T4e04bc0447ffc--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 229: Line 319:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="I46a9eab601537"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9eab601537"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 247: Line 337:


Primer 2:CCATGACTTTCTTTTTCGCGTAA  
Primer 2:CCATGACTTTCTTTTTCGCGTAA  
|-
|
[[:Category:Kohara_Phage:1G7|1G7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=478 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12F3|12F3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=501 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2F9|2F9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=502 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 284: Line 401:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="H46a9eab6a5bbb"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9eab6a5bbb"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG20080 EcoCyc:EG20080]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4141 EchoBASE:EB4141]
EcoCyc:EG20080
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2976 EcoliGenExpDB:b2976]
EcoGene:EG20080
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3705 ECOL199310CYC:C3705]
RegulonDB:ECK120002441
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG20080 EcoGene:EG20080]
[http://www.ncbi.nlm.nih.gov/gene?term=948857 GeneID:948857]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/711 CGSC:711]
EchoBASE:EB4141
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009767&formSubmitReturn=1 ASAP:ABE-0009767]
ASAP:ABE-0009767
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 355: Line 465:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="O46a706a6d3a5f"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a706a6d3a5f"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments
Line 377: Line 487:
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:glc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:glc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 19 September 2013

{{#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 Sequence Features Alleles and Phenotypes Genetic Interactions 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

glcB

Mnemonic

Glycolate

Synonyms

ECK2970, b2976, JW2943, glc[1], glc

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

67.24 minutes 

MG1655: 3121827..3119656
<gbrowseImage> name=NC_000913:3119656..3121827 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3050697..3048526
<gbrowseImage> name=NC_012967:3048526..3050697 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3006804..3008975
<gbrowseImage> name=NC_012759:3006804..3008975 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3122461..3120290
<gbrowseImage> name=NC_007779:3120290..3122461 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3219572..3217401
<gbrowseImage> name=NC_010473:3217401..3219572 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3119659

Edman degradation

PMID:7925370[2]


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

ΔglcB (Keio:JW2943)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10272[4]

ΔglcB::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[5]

glcB11

CGSC:12112

ΔglcB749::kan

PMID:16738554[3]

CGSC:101130


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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

JW2943

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAGTCAAACCATAACCCAGAG

Primer 2:CCATGACTTTCTTTTTCGCGTAA

1G7

Kohara Phage

Genobase

PMID:3038334[7]

12F3

Kohara Phage

Genobase

PMID:3038334[7]

2F9

Kohara Phage

Genobase

PMID:3038334[7]

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[4]

est. P1 cotransduction: 57% [8]

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[4]

est. P1 cotransduction: 30% [8]

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

EcoCyc:EG20080

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG20080

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002441

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948857

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4141

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009767

Escherichia coli str. K-12 substr. MG1655

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. ↑ Molina, I et al. (1994) Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme. Eur. J. Biochem. 224 541-8 PubMed
  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. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 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 7.2 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  8. ↑ 8.0 8.1 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=glcB:Gene&oldid=1479429"