selU:Gene: Difference between revisions

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Added to the category for BW2952 genes.
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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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seeded from [http://www.uniprot.org/uniprot/P33667 UniProt:P33667]  
seeded from [http://www.uniprot.org/uniprot/P33667 UniProt:P33667]  
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&Delta;ybbB::kan
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deletion
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[[Biolog]]:respiration
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unable to respire [[Carbon sources|a-Ketoglutarate]]
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PMID:16095938
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Revision as of 23:38, 10 May 2010

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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

selU

Mnemonic

Selenium

Synonyms

ECK0496, b0503, JW0491, ybbB[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

11.41 minutes 

MG1655: 530450..529356
gbrowse_img.php?coord=529356..530450&genome=ecoli&name=MG1655&trackset=0&width=300&.png

BW2952

NC_012759: 432115..433209
gbrowse_img.php?coord=432115..433209&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 530450..529356
gbrowse_img.php?coord=529356..530450&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 469781..468687
gbrowse_img.php?coord=468687..469781&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

ΔybbB (Keio:JW0491)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8636[3]

ybbB::Tn5KAN

PMID:12519969[4]

ASAP

At position 1013 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20190

ybbB::Tn5KAN

PMID:12519969[4]

ASAP

At position 1013 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20191

selUC96S

C96S

No change in activity

seeded from UniProt:P33667

selUC97S

C97S

In vivo, abolishes 2-selenouridine synthase activity. In vitro, reduces activity by only 50%

seeded from UniProt:P33667

ΔybbB::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ΔybbB786::kan

PMID:16738554[2]

CGSC:103658


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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

JW0491

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCAAGAGAGACACACGGAACA

Primer 2:CCCCGCGCCTTAACCCATTCCGC

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 34% [7]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 43% [7]
Synonyms:purE79::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:EG11768

EchoBASE (EcoliWiki Page)

EchoBASE:EB1718

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0503

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0618

EcoGene (EcoliWiki Page)

EcoGene:EG11768

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBBB

ASAP (EcoliWikiPage)

ASAP:ABE-0001740


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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. ↑ 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. ↑ 4.0 4.1 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. ↑ 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
  7. ↑ 7.0 7.1 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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