uspA:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11390 ECOCYC:EG11390]
EcoCyc:EG11390
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11390 EcoGene:EG11390]
EcoGene:EG11390
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120001357
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB1363
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0011414
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:31, 27 May 2013

{{#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

uspA

Mnemonic

Universal stress protein

Synonyms

ECK3480, b3495, JW3462[1], JW3462

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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

78.41 minutes, 78.41 minutes 

MG1655: 3638134..3638568
<gbrowseImage> name=NC_000913:3638134..3638568 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3570800..3571234
<gbrowseImage> name=NC_012967:3570800..3571234 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3526628..3527062
<gbrowseImage> name=NC_012759:3526628..3527062 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4000304..3999870
<gbrowseImage> name=AC_000091:3999870..4000304 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3735879..3736313
<gbrowseImage> name=NC_010473:3735879..3736313 source=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

3638137

Edman degradation

PMID:1453957[2]
PMID:8506346[3]
PMID:8740179[4]
PMID:9298646[5]
PMID:9405142[6]


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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

ΔuspA (Keio:JW3462)

deletion

deletion

PMID:16738554[7]

Shigen
CGSC10565[8]

uspA1::kan

PMID:8391533[9]

CGSC:28130

ΔuspA751::kan

PMID:16738554[7]

CGSC:103334


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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

JW3462

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCGCTTATAAACACATTCTCAT

Primer 2:CCTTCTTCTTCGTCGCGCAGCGG

12E4

Kohara Phage

Genobase

PMID:3038334[11]

6A4

Kohara Phage

Genobase

PMID:3038334[11]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[8]

est. P1 cotransduction: 12% [12]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[8]

est. P1 cotransduction: % [12]

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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

EcoCyc:EG11390

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11390

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948007

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001357

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1363

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011414

Escherichia coli str. K-12 substr. MG1655

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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. ↑ Nyström, T & Neidhardt, FC (1992) Cloning, mapping and nucleotide sequencing of a gene encoding a universal stress protein in Escherichia coli. Mol. Microbiol. 6 3187-98 PubMed
  3. ↑ Henzel, WJ et al. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 90 5011-5 PubMed
  4. ↑ Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 PubMed
  5. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  6. ↑ Freestone, P et al. (1997) The universal stress protein, UspA, of Escherichia coli is phosphorylated in response to stasis. J. Mol. Biol. 274 318-24 PubMed
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 8.2 CGSC: The Coli Genetics Stock Center
  9. ↑ Nyström, T & Neidhardt, FC (1993) Isolation and properties of a mutant of Escherichia coli with an insertional inactivation of the uspA gene, which encodes a universal stress protein. J. Bacteriol. 175 3949-56 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  12. ↑ 12.0 12.1 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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