ompF: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

ompF

Mnemonic

Outer membrane protein

Synonyms

ECK0920, b0929, JW0912, cmlB, coa, cry, tolF, nfxB?[1][2]

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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

21.23 minutes 

MG1655: 986205..985117
<gbrowseImage> name=NC_000913:985117..986205 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1004074..1002986
<gbrowseImage> name=NC_012967:1002986..1004074 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 888085..889173
<gbrowseImage> name=NC_012759:888085..889173 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 987404..986316
<gbrowseImage> name=AC_000091:986316..987404 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1040133..1039045
<gbrowseImage> name=NC_010473:1039045..1040133 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

985120

Edman degradation

PMID:7001461[3]
PMID:9298646[4]
PMID:9629924[5]


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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

ΔompF (Keio:JW0912)

deletion

deletion

PMID:16738554[6]

Shigen
CGSC8925[7]

ompF627(T2R)

T2 resistant

PMID:3286621[8]

CGSC:4722

ompF626

CGSC:6264

ompF254

CGSC:6819

ompF625

CGSC:11640

ΔompF746::kan

PMID:16738554[6]

CGSC:102178


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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

JW0912

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCATGAAGCGCAATATTCTGGC

Primer 2:CCGAACTGGTAAACGATACCCAC

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[7]

est. P1 cotransduction: 20% [10]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[7]

est. P1 cotransduction: 54% [10]

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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:EG10671

EchoBASE (EcoliWiki Page)

EchoBASE:EB0665

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0929

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1071

EcoGene (EcoliWiki Page)

EcoGene:EG10671

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:OMPF

CGSC (EcoliWiki Page)

CGSC:435

ASAP (EcoliWikiPage)

ASAP:ABE-0003153


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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Chen, R et al. (1980) Primary structure of major outer membrane protein II (ompA protein) of Escherichia coli K-12. Proc. Natl. Acad. Sci. U.S.A. 77 4592-6 PubMed
  4. ↑ 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
  5. ↑ Molloy, MP et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 837-44 PubMed
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 7.2 CGSC: The Coli Genetics Stock Center
  8. ↑ Black, PN (1988) The fadL gene product of Escherichia coli is an outer membrane protein required for uptake of long-chain fatty acids and involved in sensitivity to bacteriophage T2. J. Bacteriol. 170 2850-4 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 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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