ompA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php
Convert to gbrowse_img.php extension.
Line 75: Line 75:
21.95 minutes 
21.95 minutes 
|
|
MG1655: 1019276..1018236<br />{{GBrowseFigureByCoord|1018236|1019276|ecoli|MG1655}}
MG1655: 1019276..1018236<br /><gbrowseImage>
name=NC_000913:1018236..1019276
source=ecoli
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10669 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10669 EcoCyc]
Line 89: Line 94:


|
|
NC_012967: 1037144..1036104<br />{{GBrowseFigureByCoord|1036104|1037144|REL606|NC_012967}}
NC_012967: 1037144..1036104<br /><gbrowseImage>
name=NC_012967:1036104..1037144
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|1036104|1037144|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1036104|1037144|GBrowse (REL606)}}
Line 100: Line 110:


|
|
NC_012759: 921204..922244<br />{{GBrowseFigureByCoord|921204|922244|BW2952|NC_012759}}
NC_012759: 921204..922244<br /><gbrowseImage>
name=NC_012759:921204..922244
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|BW2952|012759|921204|NC_922244|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|012759|921204|NC_922244|GBrowse (BW2952)}}
Line 111: Line 126:
&nbsp;
&nbsp;
|
|
W3110: 1020475..1019435<br />{{GBrowseFigureByCoord|1019435|1020475|ecoli_W3110|W3110}}
W3110: 1020475..1019435<br /><gbrowseImage>
name=AC_000091:1019435..1020475
source=ecoli_W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1018435|1021475|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|AC_000091|1018435|1021475|GBrowse(W3110)}}  
Line 122: Line 142:


|
|
DH10B: 1073204..1072164<br />{{GBrowseFigureByCoord|1072164|1073204|ecoli_DH10B|DH10B}}
DH10B: 1073204..1072164<br /><gbrowseImage>
name=NC_010473:1072164..1073204
source=ecoli_DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1070084|1075284|GBrowse(DH10B)}}
{{GBrowseLink|ecoli_DH10B|NC_010473|1070084|1075284|GBrowse(DH10B)}}

Revision as of 21:25, 26 July 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 Sequence Features Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


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]

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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>

edit table


Notes

Sequence Features

[back to top]


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]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

PMID:12519969[9]

ASAP

At position 518 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20072

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


edit table


Notes

Genetic Resources

[back to top]


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]

edit table


Notes

Accessions in Other Databases

[back to top]


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


edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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).

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ompA:Gene&oldid=1178365"