yaeF:Gene: Difference between revisions

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{|  id="I46a9aa8b4da4c"  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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At position 155 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20035  
At position 155 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20035  
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&Delta;yaeF::kan
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deletion
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[[Biolog]]:respiration
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unable to respire [[Carbon sources|Acetate]]
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PMID:16095938
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[[cgscmutation:103480|CGSC:103480]]
[[cgscmutation:103480|CGSC:103480]]
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&Delta;yaeF::kan
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deletion
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[[Biolog]]:respiration
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unable to respire [[Carbon sources|Acetate]]
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PMID:16095938
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Revision as of 23:36, 10 May 2010

{{#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 Alleles and Phenotypes 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

yaeF

Mnemonic

Systematic nomenclature

Synonyms

ECK0193, b0193, JW5016, yaeK[1]

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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

4.66 minutes 

MG1655: 217003..216179
gbrowse_img.php?coord=216179..217003&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 219845..219021
gbrowse_img.php?coord=219021..219845&genome=REL606&name=NC_012967&trackset=0&width=300&.png

BW2952

NC_012759: 216178..217002
gbrowse_img.php?coord=216178..217002&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 217003..216179
gbrowse_img.php?coord=216179..217003&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 191107..190283
gbrowse_img.php?coord=190283..191107&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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

ΔyaeF (Keio:JW5016)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11130[3]

yaeF::Tn5KAN

PMID:12519969[4]

ASAP

At position 155 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20035

ΔyaeF::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

yaeF-1::FLKP2(lacZ,kan,Plac)

PMID:12142427[6]

CGSC:87198

ΔyaeF-2

PMID:12142427[6]

CGSC:87200

ΔyaeF-790::kan

PMID:16738554[2]

CGSC:103480


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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

JW5016

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGATAAACCAAAGGCGTACTG

Primer 2:CCaCGGGTCAAACCAACAAAGCG

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 2% [8]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 57% [8]
Synonyms:zae-502::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:EG12138

EchoBASE (EcoliWiki Page)

EchoBASE:EB2059

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0193

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0234

EcoGene (EcoliWiki Page)

EcoGene:EG12138

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAEF

ASAP (EcoliWikiPage)

ASAP:ABE-0000655


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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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  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
  6. ↑ 6.0 6.1 Merlin, C et al. (2002) Tools for characterization of Escherichia coli genes of unknown function. J. Bacteriol. 184 4573-81 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 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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