epd:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|epd}}{{Tab On|Gene|epd}}{{Tab|Gene Product(s)|epd}}{{Tab|Expression|epd}}{{Tab|Evolution|epd}}{{Tab|On One Page|epd}}{{TabsBottom}}
{{Tab|Quickview|epd}}{{Tab On|Gene|epd}}{{Tab|Gene Product(s)|epd}}{{Tab|Expression|epd}}{{Tab|Evolution|epd}}{{Tab|On One Page|epd}}{{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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="E46a9e994403bf"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''epd''  
''epd''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Erythrose-4-P dehydrogenase
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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<!--Nomenclature_notes--></protect>
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===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="G46a9e994bf3fb"  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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66.18 minutes&nbsp;
66.18 minutes&nbsp;
|
|
MG1655: 3071713..3070694<br />{{GBrowseFigureByCoord|3069694|3072713|ecoli|MG1655}}
MG1655: 3071713..3070694<br /><gbrowseImage>
name=NC_000913:3070694..3071713
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10368 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10368 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3069694..3072713 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3069694|3072713|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3070694..3071713&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3070694|3071713|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10368 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10368 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2959442..2958423<br /><gbrowseImage>
name=NC_012967:2958423..2959442
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2958423|2959442|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2958423|2959442|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2957842..2958861<br /><gbrowseImage>
name=NC_012759:2957842..2958861
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2957842|2958861|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2957842|2958861|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3072347..3071328<br />{{GBrowseFigureByCoord|3070328|3073347|ecoli_W3110|W3110}}  
W3110: 3072347..3071328<br /><gbrowseImage>
name=NC_007779:3071328..3072347
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3070328|3073347|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3071328|3072347|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 3165583..3164564<br /><gbrowseImage>
name=NC_010473:3164564..3165583
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3070328..3073347 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3162526|3167621|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3071328..3072347&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3162526|3167621|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3070697
|
Edman degradation
|
PMID:7751290<br />
|
 
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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="A46a9e995c3bd6"  class=" tableEdit Gene_allele_table dataTable" 
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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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&Delta;epd (Keio:JW2894)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009607 epd::Tn5KAN-I-SceI] (FB20979)
|
Insertion at nt 643 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20979]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009607 epd::Tn5KAN-I-SceI] (FB20980)
|
Insertion at nt 643 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20980]
|
does not contain [[pKD46]]
|-
|
epdC155A,G,V
|
 
|
C155A,G,V
|
 
|
No significant activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9B6 UniProt:P0A9B6]
|-
|
epdH182N
|
 
|
H182N
|
 
|
10-fold reduction in activity. Increases affinity for D-erythrose-4- phosphate and reduces affinity for glyceraldehyde 3-phosphate
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9B6 UniProt:P0A9B6]
|-
|
epdC316A,Y
|
 
|
C316A,Y
|
 
|
Reduces activity and affinity for D-erythrose-4-phosphate and increases affinity for glyceraldehyde 3-phosphate
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9B6 UniProt:P0A9B6]
|-
|
''&#916;epd-11::Ery''
|
 
|
 
|
 
|
 
|
PMID:9260967
|
[[cgscmutation:60142|CGSC:60142]]
|
 
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<protect><!--Alleles_notes--></protect>
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===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="D4e04ba716a875"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2894
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCACCGTACGCGTAGCGATAAA
 
Primer 2:CCtCTGAAAGCAACAGTAGCCAT
|-
|
[[:Category:Kohara_Phage:6C5|6C5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=472 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1H10|1H10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=473 Genobase]
|
PMID:3038334
|-
|
[[recD:Gene|recD1901::Tn10]]
|
Linked marker
|
CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[speA:Gene|speA210::Tn10]]
|
Linked marker
|
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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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=EG10368 EcoCyc:EG10368] 
EcoCyc:EG10368
|
|
''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=EB0363 EchoBASE:EB0363] 
EcoGene:EG10368
|
|
''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=b2927 EcoliGenExpDB:b2927] 
RegulonDB:ECK120000361
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|-  
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C3505 ECOL199310CYC:C3505] 
|
|-
|
|
[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=EG10368 EcoGene:EG10368]
[http://www.ncbi.nlm.nih.gov/gene?term=947413 GeneID:947413]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=EPD ECOO157CYC:EPD] 
EchoBASE:EB0363
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/32089 CGSC:32089] 
ASAP:ABE-0009607
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:epd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

epd

Mnemonic

Erythrose-4-P dehydrogenase

Synonyms

ECK2923, b2927, JW2894, gapB, gap2[1][2]

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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

66.18 minutes 

MG1655: 3071713..3070694
<gbrowseImage> name=NC_000913:3070694..3071713 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2959442..2958423
<gbrowseImage> name=NC_012967:2958423..2959442 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2957842..2958861
<gbrowseImage> name=NC_012759:2957842..2958861 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3072347..3071328
<gbrowseImage> name=NC_007779:3071328..3072347 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3165583..3164564
<gbrowseImage> name=NC_010473:3164564..3165583 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

Coding Start (SO:0000323)

MG1655

3070697

Edman degradation

PMID:7751290[3]


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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

Δepd (Keio:JW2894)

deletion

deletion

PMID:16738554[4]

Shigen

epd::Tn5KAN-I-SceI (FB20979)

Insertion at nt 643 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20979

contains pKD46

epd::Tn5KAN-I-SceI (FB20980)

Insertion at nt 643 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20980

does not contain pKD46

epdC155A,G,V

C155A,G,V

No significant activity

seeded from UniProt:P0A9B6

epdH182N

H182N

10-fold reduction in activity. Increases affinity for D-erythrose-4- phosphate and reduces affinity for glyceraldehyde 3-phosphate

seeded from UniProt:P0A9B6

epdC316A,Y

C316A,Y

Reduces activity and affinity for D-erythrose-4-phosphate and increases affinity for glyceraldehyde 3-phosphate

seeded from UniProt:P0A9B6

Δepd-11::Ery

PMID:9260967[6]

CGSC:60142


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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

JW2894

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACCGTACGCGTAGCGATAAA

Primer 2:CCtCTGAAAGCAACAGTAGCCAT

6C5

Kohara Phage

Genobase

PMID:3038334[8]

1H10

Kohara Phage

Genobase

PMID:3038334[8]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[9]

est. P1 cotransduction: % [10]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[9]

est. P1 cotransduction: 60% [10]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

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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:EG10368

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10368

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000361

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947413

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0363

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009607

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Zhao, G et al. (1995) Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis. J. Bacteriol. 177 2804-12 PubMed
  4. ↑ 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
  5. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ Seta, FD et al. (1997) Characterization of Escherichia coli strains with gapA and gapB genes deleted. J. Bacteriol. 179 5218-21 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. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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