gpmM: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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{| id="E46a9fa5d511d6"  class=" tableEdit Gene_nomenclature_table"   
{|   id="E46a9fa5d511d6"  class=" tableEdit Gene_nomenclature_table"   


|-
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''gpmI, ECK3602, b3612, JW3587, yibO, pmgI, gpmC, pgmI''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''gpmI, ECK3602, b3612, JW3587, yibO, pmgI, gpmC, pgmI''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, pgmI''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="E46a9fa5dd3602"  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="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
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81.54 minutes&nbsp;
81.54 minutes&nbsp;
|
|
MG1655: 3783283..3784827<br />{{GBrowseFigureByCoord|3783283|3784827|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]
{{GBrowseLink|ecoli|NC_000913|3782283|3785827|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3782283|3785827|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3783283|3784827|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]  
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|
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NC_012967: 3726026..3727570<br />{{GBrowseFigureByCoord|3726026|3727570|REL606|NC_012967}}
NC_012967: 3726026..3727570<br /><gbrowseImage>
name=NC_012967:3726026..3727570
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|REL606|NC_012967|3726026|3727570|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3726026|3727570|GBrowse (REL606)}}
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W3110
[[BW2952]]
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&nbsp;
 
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W3110: 3855155..3853611<br />{{GBrowseFigureByCoord|3853611|3855155|ecoli_W3110|W3110}}
NC_012759: 3671609..3673153<br /><gbrowseImage>
name=NC_012759:3671609..3673153
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|3852611|3856155|GBrowse(W3110)}}  
{{GBrowseLink|BW2952|NC_012759|3671609|3673153|GBrowse (BW2952)}}
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3853611|3855155|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3671609|3673153|FASTA Dump}}  
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[[BW2952]]
W3110
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&nbsp;
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W3110: 3855155..3853611<br /><gbrowseImage>
name=NC_007779:3853611..3855155
source=W3110
preset=GeneLocation
</gbrowseImage>


|
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NC_012759: 3671609..3673153<br />{{GBrowseFigureByCoord|3671609|3673153|BW2952|NC_012759}}
{{GBrowseLink|W3110|NC_007779|3852611|3856155|GBrowse(W3110)}}  
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{{GBrowseLink|BW2952|012759|3671609|NC_3673153|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3671609|NC_3673153|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3853611|3855155|FASTA Dump}}  


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{|   id="Q46a9fa5e96441"  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="Q46a9fa5e96441"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17779.Q46a9fa5e96441&page=17779&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
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{| {{Prettytable}} id="K46a9fa5edfd39"  class=" tableEdit Gene_allele_table dataTable"   
{| 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}}
|- {{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
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011818 yibO]
[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
|
|


|
|
PMID:12519969
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
|
[[asapstrains:ASAP|ASAP]]
 
|
|
At position 1343 in Plus orientation, contains plasmid [[pKD46]].<br />ASAP strain name: FB21341
   
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011818 yibO]
&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
|
|


|
|
PMID:12519969
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
|
[[asapstrains:ASAP|ASAP]]
 
|
|
At position 1343 in Plus orientation, does not contain plasmid [[pKD46]].<br />ASAP strain name: FB21342
   
|-  
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[[Biolog]]:respiration
[[Biolog]]:respiration
|
|
unable to respire [[Carbon sources|Acetate]]
unable to respire [[Carbon sources|L-Aspartate]]
|
|
PMID:16095938
PMID:16095938
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&Delta;yibO::kan
gpmM
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deletion
deletion
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[[Biolog]]:respiration
Sensitivity to
|
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
increases sensitivity to bicyclomycin
|
|
PMID:16095938
PMID:21357484
|
|


|
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fig 2


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17779.L4e04bc8953fed-->
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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
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="J46a9fa5fa2f0b"  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="J46a9fa5fa2f0b"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:  
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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{|   id="Z46a9fa604d258"  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="Z46a9fa604d258"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12296 EcoCyc:EG12296]
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|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2204 EchoBASE:EB2204]
EcoCyc:EG12296
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3612 EcoliGenExpDB:b3612]
EcoGene:EG12296
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
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[http://BioCyc.org/ECOL199310/new-image?object=C4438 ECOL199310CYC:C4438]
RegulonDB:ECK120002177
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[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=EG12296 EcoGene:EG12296]
[http://www.ncbi.nlm.nih.gov/gene?term=948130 GeneID:948130]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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|
[http://BioCyc.org/ECOO157/new-image?object=YIBO ECOO157CYC:YIBO]
EchoBASE:EB2204
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011818&formSubmitReturn=1 ASAP:ABE-0011818]
ASAP:ABE-0011818
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:48, 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

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

[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

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

[back to top]


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

[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

Plasmid clone

Shigen

PMID:16769691[7]

Status:

Primer 1:

Primer 2:

5D2

Kohara Phage

Genobase

PMID:3038334[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: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

[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 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

Categories

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