ompA:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
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|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
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|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:51, 24 June 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

ompA

Mnemonic

Outer membrane protein

Synonyms

ECK0948, b0957, JW0940, con, tolG, tut[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

21.95 minutes 

MG1655: 1019276..1018236
<gbrowseImage> name=NC_000913:1018236..1019276 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1037144..1036104
<gbrowseImage> name=NC_012967:1036104..1037144 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 921204..922244
<gbrowseImage> name=NC_012759:921204..922244 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1020475..1019435
<gbrowseImage> name=AC_000091:1019435..1020475 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1073204..1072164
<gbrowseImage> name=NC_010473:1072164..1073204 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

1018239

Edman degradation

PMID:340230[2]
PMID:7001461[3]
PMID:8740179[4]
PMID:9298646[5]
PMID:9629924[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

ΔompA (Keio:JW0940)

deletion

deletion

PMID:16738554[7]

Shigen
CGSC8942[8]

ompA::Tn5KAN-2 (FB20072)

Insertion at nt 518 in Minus orientation

PMID:15262929[9]

E. coli Genome Project:FB20072

does not contain pKD46

ΔompA::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[10]

ompA252

CGSC:9906

ompA256

CGSC:9910

ΔompA772::kan

PMID:16738554[7]

CGSC:102174


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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

JW0940

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCAAAAAGACAGCTATCGCGAT

Primer 2:CCAGCCTGCGGCTGAGTTACAA

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[8]

est. P1 cotransduction: 57% [12]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[8]

est. P1 cotransduction: 14% [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 (EcoliWiki Page)

EcoCyc:EG10669

EchoBASE (EcoliWiki Page)

EchoBASE:EB0663

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0957

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1093

EcoGene (EcoliWiki Page)

EcoGene:EG10669

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:OMPA

CGSC (EcoliWiki Page)

CGSC:437

ASAP (EcoliWikiPage)

ASAP:ABE-0003240


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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. ↑ Schweizer, M et al. (1978) Major proteins of the Escherichia coli outer cell envelope membrane. Interaction of protein II with lipopolysaccharide. Eur. J. Biochem. 82 211-7 PubMed
  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. ↑ 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. ↑ Molloy, MP et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 837-44 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  10. ↑ 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
  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 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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