ispU:Gene: Difference between revisions

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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''ispU''  
''ispU''
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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Isoprenoid
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0173, b0174, JW0169, uppS, rth, yaeS''<ref name='LIB:Riley_2006'/>
''ECK0173, b0174, JW0169, uppS, rth, yaeS''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature type!!Location!!Description
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Decrease in activity; reduced affinity for decaprenyl diphosphate substrate analog
Decrease in activity; reduced affinity for decaprenyl diphosphate substrate analog
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seeded from [http://www.uniprot.org/uniprot/P60472 UniProt:P60472]
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uppSD223A
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D223A
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No effect
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Great decrease in activity; reduced affinity for IPP
Great decrease in activity; reduced affinity for IPP
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seeded from [http://www.uniprot.org/uniprot/P60472 UniProt:P60472]
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uppSD223A
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D223A
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No effect
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Revision as of 21:21, 25 February 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

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
gbrowse_img.php?coord=194903..195664&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 197745..198506
gbrowse_img.php?coord=197745..198506&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 194903..195664
gbrowse_img.php?coord=194903..195664&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 169007..169768
gbrowse_img.php?coord=169007..169768&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 Location Description
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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[2]

Status:Clone OK

Primer 1:GCCATGTTGTCTGCTACTCAACC

Primer 2:CCGGCTGTTTCATCACCGGGCTC

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 12% [4]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 22% [4]
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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<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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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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