ispU:Gene: Difference between revisions

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Revision as of 21:05, 26 July 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 Sequence Features 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

ispU

Mnemonic

Isoprenoid

Synonyms

ECK0173, b0174, JW0169, uppS, rth, yaeS[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

4.2 minutes 

MG1655: 194903..195664
<gbrowseImage> name=NC_000913:194903..195664 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 197745..198506
<gbrowseImage> name=NC_012967:197745..198506 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 194902..195663
<gbrowseImage> name=NC_012759:194902..195663 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 194903..195664
<gbrowseImage> name=AC_000091:194903..195664 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 169007..169768
<gbrowseImage> name=NC_010473:169007..169768 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

194903

Edman degradation

PMID:9882662[2]


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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

uppSD26A

D26A

Great decrease in activity

seeded from UniProt:P60472

uppSL137A

L137A

Formation predominantly of a C(70) polymer rather than the C(55) polymer

seeded from UniProt:P60472

uppSD190A

D190A

No effect

seeded from UniProt:P60472

uppSW75A,F

W75A,F

Decrease in activity; reduced affinity for decaprenyl diphosphate substrate analog

seeded from UniProt:P60472

uppSD223A

D223A

No effect

seeded from UniProt:P60472

uppSD218A

D218A

Slight decrease in activity

seeded from UniProt:P60472

uppSW221F

W221F

Decrease in affinity for IPP

seeded from UniProt:P60472

uppSE81A

E81A

Slight decrease in activity

seeded from UniProt:P60472

uppSW31F

W31F

Decrease in activity; reduced affinity for decaprenyl diphosphate substrate analog

seeded from UniProt:P60472

uppSW91F

W91F

Decrease in affinity for IPP

seeded from UniProt:P60472

uppSW149F

W149F

Decrease in affinity for IPP

seeded from UniProt:P60472

uppSA143V

A143V

No effect on polymer length

seeded from UniProt:P60472

uppSI62A

I62A

Formation predominantly of C(60) and C(65) polymers rather than the C(55) polymer

seeded from UniProt:P60472

uppSH103A

H103A

No effect

seeded from UniProt:P60472

uppSA69L

A69L

Produces shorter polymers

seeded from UniProt:P60472

uppSS71A

S71A

Decrease in activity

seeded from UniProt:P60472

uppSE73A

E73A

Slight decrease in activity

seeded from UniProt:P60472

uppSN74A

N74A

Decrease in activity

seeded from UniProt:P60472

uppSR77A

R77A

Decrease in activity

seeded from UniProt:P60472

uppSV105A

V105A

Formation predominantly of C(60), C(65) and C(70) polymers rather than the C(55) polymer

seeded from UniProt:P60472

uppSD150A

D150A

Great decrease in affinity for the substrate

seeded from UniProt:P60472

uppSE198A

E198A

No effect

seeded from UniProt:P60472

uppSW207F

W207F

Decrease in affinity for both IPP and decaprenyl diphosphate substrate analog

seeded from UniProt:P60472

uppSE213A

E213A

Great decrease in activity; reduced affinity for IPP

seeded from UniProt:P60472

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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

JW0169

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCATGTTGTCTGCTACTCAACC

Primer 2:CCGGCTGTTTCATCACCGGGCTC

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[4]

est. P1 cotransduction: 12% [5]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[4]

est. P1 cotransduction: 22% [5]
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:G6092

EchoBASE (EcoliWiki Page)

EchoBASE:EB3113

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0174

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0211

EcoGene (EcoliWiki Page)

EcoGene:EG13329

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAES

ASAP (EcoliWikiPage)

ASAP:ABE-0000595


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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. ↑ Apfel, CM et al. (1999) Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential uppS gene. J. Bacteriol. 181 483-92 PubMed
  3. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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