pgm:Gene: Difference between revisions

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|{{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]]
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{|{{Prettytable}}
{|   id="H46a9b68649ad9"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''pgm''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''pgm''
Phophoglucomutase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0676, b0688, JW0675, blu''<ref name='LIB:Riley_2006'/>, blu, pgmA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11929.H46a9b68649ad9&page=11929&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0676, b0688, JW0675, blu''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128987'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9b686c0f10"  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
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MG1655
MG1655
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15.36 minutes&nbsp;
15.36 minutes&nbsp;
|
|
MG1655: 712781..714421<br />{{GBrowseFigureByCoord|711781|715421|ecoli|MG1655}}
MG1655: 712781..714421<br /><gbrowseImage>
name=NC_000913:712781..714421
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12144 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12144 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:711781..715421 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|711781|715421|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:712781..714421&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|712781|714421|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12144 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12144 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 695653..697293<br /><gbrowseImage>
name=NC_012967:695653..697293
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|695653|697293|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|695653|697293|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 615541..617181<br /><gbrowseImage>
name=NC_012759:615541..617181
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|615541|617181|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|615541|617181|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 713980..715620<br />{{GBrowseFigureByCoord|712980|716620|ecoli_W3110|W3110}}  
W3110: 713980..715620<br /><gbrowseImage>
name=NC_007779:713980..715620
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|712980|716620|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|713980|715620|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:712980..716620 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:713980..715620&plugin_action=Go FASTA Dump]
 
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DH10B: 765373..767013<br /><gbrowseImage>
name=NC_010473:765373..767013
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|762093|770293|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|762093|770293|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z46a9b687a8e2c"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!|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
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107042 CGSC8761]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107042 CGSC8761]<ref name='LIB:cgsc'/>  
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''pgm-67''
|
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[[cgscmutation:6538|CGSC:6538]]
|
|-
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''pgm-3''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:14474|CGSC:14474]]
|
|-
|
''pgm-191''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:14476|CGSC:14476]]
|
|-
|
''&#916;pgm-736::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102312|CGSC:102312]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0675
JW0675
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[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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCCGCGTTTTTCAGAACTTCGCT  
Primer 2:CCCGCGTTTTTCAGAACTTCGCT  
|-
|-
|
[[:Category:Kohara_Phage:3A6|3A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=172 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11A10|11A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=173 Genobase]
|
PMID:3038334
|-  
|
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[[asnB:Gene|asnB3057::Tn10]]
[[asnB:Gene|asnB3057::Tn10]]
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CAG18433 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39394 CGSC7349]<ref name='LIB:cgsc'/>
CAG18433 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39394 CGSC7349]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.  
Synonyms:zbf-3057::Tn10  
|-  
 
 
The Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.  
|-
|
|
[[nadA:Gene|nadA57::Tn10]]
[[nadA:Gene|nadA57::Tn10]]
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|
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est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12144 EcoCyc:EG12144] 
EcoCyc:EG12144
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2065 EchoBASE:EB2065] 
EcoGene:EG12144
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0688 EcoliGenExpDB:b0688] 
RegulonDB:ECK120002045
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0775 ECOL199310CYC:C0775]
[http://www.ncbi.nlm.nih.gov/gene?term=945271 GeneID:945271]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12144 EcoGene:EG12144] 
EchoBASE:EB2065
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PGM ECOO157CYC:PGM] 
ASAP:ABE-0002345
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11929.B46a9b688d995c&page=11929&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/406 CGSC:406] 
|
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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:pgm genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 19 September 2013

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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

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

Standard name

pgm

Mnemonic

Phophoglucomutase

Synonyms

ECK0676, b0688, JW0675, blu[1], blu, pgmA

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Notes

Cloned and sequenced by Lu and Kleckner[2]

Location(s) and DNA Sequence

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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

15.36 minutes 

MG1655: 712781..714421
<gbrowseImage> name=NC_000913:712781..714421 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 695653..697293
<gbrowseImage> name=NC_012967:695653..697293 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 615541..617181
<gbrowseImage> name=NC_012759:615541..617181 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 713980..715620
<gbrowseImage> name=NC_007779:713980..715620 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 765373..767013
<gbrowseImage> name=NC_010473:765373..767013 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

Δpgm (Keio:JW0675)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8761[4]

pgm-1

CGSC:6535

pgm-67

CGSC:6538

pgm-3

CGSC:14474

pgm-191

CGSC:14476

Δpgm-736::kan

PMID:16738554[3]

CGSC:102312


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Notes

Genetic Interactions

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

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW0675

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGCAATCCACAATCGTGCAGG

Primer 2:CCCGCGTTTTTCAGAACTTCGCT

3A6

Kohara Phage

Genobase

PMID:3038334[6]

11A10

Kohara Phage

Genobase

PMID:3038334[6]

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[4]

est. P1 cotransduction: 66% [7]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[4]

est. P1 cotransduction: 2% [7]

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc

EcoCyc:EG12144

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12144

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002045

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945271

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2065

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002345

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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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. ↑ Lu, M & Kleckner, N (1994) Molecular cloning and characterization of the pgm gene encoding phosphoglucomutase of Escherichia coli. J. Bacteriol. 176 5847-51 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. ↑ 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 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
  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

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