ompF:Gene: Difference between revisions

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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=218 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=218 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:11F5|11F5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=219 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:11F5|11F5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=219 Genobase]
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PMID:3038334


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10671 EcoCyc:EG10671]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0665 EchoBASE:EB0665]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0929 EcoliGenExpDB:b0929]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C1071 ECOL199310CYC:C1071]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10671 EcoGene:EG10671]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=OMPF ECOO157CYC:OMPF]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/435 CGSC:435]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003153&formSubmitReturn=1 ASAP:ABE-0003153]
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Revision as of 20:56, 21 September 2011

{{#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

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=MG1655 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=W3110 preset=GeneLocation </gbrowseImage>

DH10B

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

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

ompFp9

protein expression

OmpF is constitutively expressed in ompFp9 mutants, there is less repression than in wild-type strain

PMID:7007334[9]


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Notes

Reduced levels of OmpF gives multiple antibiotic resistance. [10]


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

JW0912

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCATGAAGCGCAATATTCTGGC

Primer 2:CCGAACTGGTAAACGATACCCAC

E1D1

Kohara Phage

Genobase

PMID:3038334[12]

11F5

Kohara Phage

Genobase

PMID:3038334[12]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[7]

est. P1 cotransduction: 20% [13]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[7]

est. P1 cotransduction: 54% [13]

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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
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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. ↑ 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. ↑ Sato, T & Yura, T (1981) Regulatory mutations conferring constitutive synthesis of major outer membrane proteins (OmpC and OmpF) in Escherichia coli. J. Bacteriol. 145 88-96 PubMed
  10. ↑ Delihas, N & Forst, S (2001) MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors. J. Mol. Biol. 313 1-12 PubMed
  11. ↑ 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
  12. ↑ 12.0 12.1 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
  13. ↑ 13.0 13.1 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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