epd:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
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|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:25, 24 June 2011

{{#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

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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=ecoli 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=AC_000091:3071328..3072347 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

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

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[8]

est. P1 cotransduction: % [9]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[8]

est. P1 cotransduction: 60% [9]
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 (EcoliWiki Page)

EcoCyc:EG10368

EchoBASE (EcoliWiki Page)

EchoBASE:EB0363

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2927

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3505

EcoGene (EcoliWiki Page)

EcoGene:EG10368

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:EPD

CGSC (EcoliWiki Page)

CGSC:32089

ASAP (EcoliWikiPage)

ASAP:ABE-0009607


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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 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 CGSC: The Coli Genetics Stock Center
  9. ↑ 9.0 9.1 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).

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