ompT:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''ompT''  
''ompT''  
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!align=left {{table_heading_style}} |Mnemonic
!align=left |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
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''ECK0557, b0565, JW0554''<ref name='LIB:Riley_2006'/>
''ECK0557, b0565, JW0554''<ref name='LIB:Riley_2006'/>


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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/sequence?object=EG10673 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10673 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 560031..560984<br />{{GBrowseFigureByCoord|560031|560984|REL606|NC_012967}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|634589|639354|FASTA Dump}}  
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[[REL606]]
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NC_012967: 560031..560984<br />{{GBrowseFigureByCoord|560031|560984|REL606|NC_012967}}
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Synonyms:zbd-601::Tn10, zbe-601::Tn10  
Synonyms:zbd-601::Tn10, zbe-601::Tn10  


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Revision as of 02:30, 9 January 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

ompT

Mnemonic
Synonyms

ECK0557, b0565, JW0554[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

12.58 minutes 

MG1655: 584856..583903
gbrowse_img.php?coord=583903..584856&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 560031..560984
gbrowse_img.php?coord=560031..560984&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 584856..583903
gbrowse_img.php?coord=583903..584856&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 524188..523235
gbrowse_img.php?coord=523235..524188&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

DH10B

DH10B: 637448..636495
gbrowse_img.php?coord=636495..637448&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

ΔompT (Keio:JW0554)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8680[3]

ΔompT

deletion

deletion

lack ompT protease activity. lack the ability to cleave between specific paired basic amino acids

PMID:17880914[4]

ΔompT504

CGSC:28510

ompT1000::kan

CGSC:30156

ΔompT774::kan

PMID:16738554[2]

CGSC:102186


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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

JW0554

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCCGGGCGAAACTTCTGGGAAT

Primer 2:CCAAATGTGTACTTAAGACCAGC

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 28% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 9% [6]
Synonyms:zbd-601::Tn10, zbe-601::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:EG10673

EchoBASE (EcoliWiki Page)

EchoBASE:EB0667

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0565

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0652

EcoGene (EcoliWiki Page)

EcoGene:EG10673

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z1931

CGSC (EcoliWiki Page)

CGSC:4984

ASAP (EcoliWikiPage)

ASAP:ABE-0001931


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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. ↑ 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. ↑ Bishop, RE (2008) Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane. Biochim. Biophys. Acta 1778 1881-96 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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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