gpmM:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|gpmM}}{{Tab On|Gene|gpmM}}{{Tab|Gene Product(s)|gpmM}}{{Tab|Expression|gpmM}}{{Tab|Evolution|gpmM}}{{Tab|On One Page|gpmM}}{{TabsBottom}}
{{Tab|Quickview|gpmM}}{{Tab On|Gene|gpmM}}{{Tab|Gene Product(s)|gpmM}}{{Tab|Expression|gpmM}}{{Tab|Evolution|gpmM}}{{Tab|On One Page|gpmM}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''gpmM''  
''gpmM''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Glycerol P mutase, Mn-dependent
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''gpmI, ECK3602, b3612, JW3587, yibO, pmgI, gpmC, pgmI''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, pgmI''


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!{{table_heading_style}} |Synonyms
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''gpmI, ECK3602, b3612, JW3587, yibO, pmgI, gpmC, pgmI''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9fa5dd3602"  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
|-
|-  
|
|
MG1655
MG1655
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81.54 minutes&nbsp;
81.54 minutes&nbsp;
|
|
MG1655: 3783283..3784827<br />{{GBrowseFigureByCoord|3782283|3785827|ecoli|MG1655}}
MG1655: 3783283..3784827<br /><gbrowseImage>
name=NC_000913:3783283..3784827
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12296 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12296 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3782283..3785827 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3782283|3785827|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3783283..3784827&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3783283|3784827|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12296 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12296 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3726026..3727570<br /><gbrowseImage>
name=NC_012967:3726026..3727570
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3726026|3727570|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3726026|3727570|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3671609..3673153<br /><gbrowseImage>
name=NC_012759:3671609..3673153
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3671609|3673153|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3671609|3673153|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3855155..3853611<br />{{GBrowseFigureByCoord|3852611|3856155|ecoli_W3110|W3110}}
W3110: 3855155..3853611<br /><gbrowseImage>
name=NC_007779:3853611..3855155
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3852611..3856155 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3852611|3856155|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3853611..3855155&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3853611|3855155|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9fa5e96441"  class=" tableEdit Gene_sequence_features_table" 
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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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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9fa5edfd39"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011818 yibO::Tn5KAN-2] (FB21341)
|
Insertion at nt 1343 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21341]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011818 yibO::Tn5KAN-2] (FB21342)
|
Insertion at nt 1343 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21342]
|
does not contain [[pKD46]]
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Succinate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yibO::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Aspartate]]
|
PMID:16095938
|
 
|
|-
|
''&#916;gpmM724::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:106202|CGSC:106202]]
|
|-
|
gpmM
|
deletion
|
 
|
Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4e04bc8953fed"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:5D2|5D2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=575 Genobase]
|
PMID:3038334
 
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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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=EG12296 EcoCyc:EG12296] 
EcoCyc:EG12296
|
|
''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=EB2204 EchoBASE:EB2204] 
EcoGene:EG12296
|
|
''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=b3612 EcoliGenExpDB:b3612] 
RegulonDB:ECK120002177
|
|
''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=C4438 ECOL199310CYC:C4438]
[http://www.ncbi.nlm.nih.gov/gene?term=948130 GeneID:948130]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12296 EcoGene:EG12296] 
EchoBASE:EB2204
|
|
''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=YIBO ECOO157CYC:YIBO] 
ASAP:ABE-0011818
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:gpm genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:48, 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

gpmM

Mnemonic

Glycerol P mutase, Mn-dependent

Synonyms

gpmI, ECK3602, b3612, JW3587, yibO, pmgI, gpmC, pgmI[1][2], pgmI

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Notes

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

81.54 minutes 

MG1655: 3783283..3784827
<gbrowseImage> name=NC_000913:3783283..3784827 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3726026..3727570
<gbrowseImage> name=NC_012967:3726026..3727570 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3671609..3673153
<gbrowseImage> name=NC_012759:3671609..3673153 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3855155..3853611
<gbrowseImage> name=NC_007779:3853611..3855155 source=W3110 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

yibO::Tn5KAN-2 (FB21341)

Insertion at nt 1343 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB21341

contains pKD46

yibO::Tn5KAN-2 (FB21342)

Insertion at nt 1343 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB21342

does not contain pKD46

ΔyibO::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔyibO::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔyibO::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔyibO::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔyibO::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔyibO::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔgpmM724::kan

PMID:16738554[5]

CGSC:106202

gpmM

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[6]

fig 2

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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

Plasmid clone

Shigen

PMID:16769691[7]

Status:

Primer 1:

Primer 2:

5D2

Kohara Phage

Genobase

PMID:3038334[8]

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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:EG12296

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12296

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002177

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948130

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2204

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011818

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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 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
  5. ↑ 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
  6. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  7. ↑ 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
  8. ↑ 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

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