ompR:Gene: Difference between revisions

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Revision as of 21:25, 26 July 2010

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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

ompR

Mnemonic

Outer membrane protein

Synonyms

ECK3392, b3405, JW3368, cry, ompB, kmt[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

76.17 minutes 

MG1655: 3534606..3533887
<gbrowseImage> name=NC_000913:3533887..3534606 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3465268..3464549
<gbrowseImage> name=NC_012967:3464549..3465268 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3421044..3421763
<gbrowseImage> name=NC_012759:3421044..3421763 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4103832..4104551
<gbrowseImage> name=AC_000091:4103832..4104551 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3632351..3631632
<gbrowseImage> name=NC_010473:3631632..3632351 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
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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

ΔompR (Keio:JW3368)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10510[3]

ompR::Tn5KAN

PMID:12519969[4]

ASAP

At position 434 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21168

ompR::Tn5KAN

PMID:12519969[4]

ASAP

At position 434 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB21169

ΔompR::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔompR::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ompR321(Am, polar)

polar

PMID:3157679[6]

CGSC:10590

amber (UAG) mutation

ΔompR739::kan

PMID:16738554[2]

CGSC:102184


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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

JW3368

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCAAGAGAACTACAAGATTCT

Primer 2:CCTGCTTTAGAGCCGTCCGGTAC

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[3]

est. P1 cotransduction: 30% [8]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[3]

est. P1 cotransduction: 32% [8]
Synonyms:zhg-3086::Tn10, zhh-21::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:EG10672

EchoBASE (EcoliWiki Page)

EchoBASE:EB0666

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3405

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4181

EcoGene (EcoliWiki Page)

EcoGene:EG10672

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:OMPR

CGSC (EcoliWiki Page)

CGSC:434

ASAP (EcoliWikiPage)

ASAP:ABE-0011110


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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. ↑ 5.0 5.1 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. ↑ Garrett, S et al. (1985) Isolation and characterization of delta ompB strains of Escherichia coli by a general method based on gene fusions. J. Bacteriol. 162 840-4 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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