ompC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ompC}}{{Tab On|Gene|ompC}}{{Tab|Gene Product(s)|ompC}}{{Tab|Expression|ompC}}{{Tab|Evolution|ompC}}{{Tab|On One Page|ompC}}{{TabsBottom}}
{{Tab|Quickview|ompC}}{{Tab On|Gene|ompC}}{{Tab|Gene Product(s)|ompC}}{{Tab|Expression|ompC}}{{Tab|Evolution|ompC}}{{Tab|On One Page|ompC}}{{TabsBottom}}
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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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==Nomenclature==
==Nomenclature==
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{|  id="N46a9d8ba0d752"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ompC''  
''ompC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Outer membrane protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2207, b2215, JW2203, meoA, par''<ref name='LIB:Riley_2006'/>, par''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14989.N46a9d8ba0d752&page=14989&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2207, b2215, JW2203, meoA, par''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9d8ba8a830"  class=" tableEdit Gene_location_table" 
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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49.78 minutes, 49.78 minutes&nbsp;
49.78 minutes, 49.78 minutes&nbsp;
|
|
MG1655: 2310771..2309668<br />{{GBrowseFigureByCoord|2308668|2311771|ecoli|MG1655}}
MG1655: 2310771..2309668<br /><gbrowseImage>
name=NC_000913:2309668..2310771
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10670 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10670 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2308668..2311771 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2308668|2311771|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2309668..2310771&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2309668|2310771|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10670 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10670 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2262685..2261750<br /><gbrowseImage>
name=NC_012967:2261750..2262685
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2261750|2262685|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2261750|2262685|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2195473..2196576<br /><gbrowseImage>
name=NC_012759:2195473..2196576
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2195473|2196576|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2195473|2196576|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2316083..2314980<br />{{GBrowseFigureByCoord|2313980|2317083|ecoli_W3110|W3110}}  
W3110: 2316083..2314980<br /><gbrowseImage>
name=NC_007779:2314980..2316083
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2313980|2317083|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2314980|2316083|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2401759..2400656<br /><gbrowseImage>
name=NC_010473:2400656..2401759
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2313980..2317083 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2398450|2403965|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2314980..2316083&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2398450|2403965|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
2309671
|
Edman degradation
|
PMID:6297988<br />PMID:9298646<br />PMID:9629924<br />
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9d8bb86487"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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''ompC(del)'' (Keio:JW2203)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108062 CGSC9781]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007321 ompC::Tn5KAN-2] (FB20710)
|
Insertion at nt 469 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20710]
|
contains [[pKD46]]
|-  
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007321 ompC::Tn5KAN-2] (FB20711)
|
Insertion at nt 469 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20711]
|
does not contain [[pKD46]]
|-
|
''ompC171''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6820|CGSC:6820]]
|
|-
|
''ompC161''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:8752|CGSC:8752]]
|
|-
|
''ompC263''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9903|CGSC:9903]]
|
|-
|
''ompC264''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9913|CGSC:9913]]
|
|-
|
''ompC262''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9918|CGSC:9918]]
|
|-
|
''ompC172''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:14635|CGSC:14635]]
|
|-
|
''ompC768(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102176|CGSC:102176]]
|
|-
|
ompCp1
|
 
|
 
|
protein expression
|
OmpC protein synthesis is constitutive, less repression in ompCp1 than in wild-type
|
PMID:7007334
|
 
|
|-
|
''ompC<sup>-</sup>''
|
insertion
|
 
|
Sensitivity to
|
Decreased Sensitivity to Micromycin B17
|
PMID:3543211
|
 
|
See table 4 for full results. 
|-
|
''ompC'' in strain CE104
|
 
|
 
|
Resistant to
|
Resistant to Me1 phage.
|
PMID:375003
|
Experimental Strain: CE104
 
Parental Strain: PC0479
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14989.X4e04c07bd0d7e-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2203
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAAGTTAAAGTACTGTCCCT
 
Primer 2:CCGAACTGGTAAACCAGACCCAG
|-
|
[[:Category:Kohara_Phage:22A6|22A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=373 Genobase]
|
PMID:3038334
|-
|
[[napA:Gene|napA722::Tn10]]
|
Linked marker
|
CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 75% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zeg-722, zei-722::Tn10
|-
|
[[atoS:Gene|atoS298::Tn10]]
|
Linked marker
|
CAG12177 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44154 CGSC7525]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 71% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10670 EcoCyc:EG10670] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0664 EchoBASE:EB0664] 
EcoCyc:EG10670
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2215 EcoliGenExpDB:b2215] 
EcoGene:EG10670
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2758 ECOL199310CYC:C2758] 
RegulonDB:ECK120000663
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://ecogene.org/geneinfo.php?eg_id=EG10670 EcoGene:EG10670]
[http://www.ncbi.nlm.nih.gov/gene?term=946716 GeneID:946716]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=OMPC ECOO157CYC:OMPC] 
EchoBASE:EB0664
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/436 CGSC:436] 
ASAP:ABE-0007321
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 19 September 2013

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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 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

ompC

Mnemonic

Outer membrane protein

Synonyms

ECK2207, b2215, JW2203, meoA, par[1], par

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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

49.78 minutes, 49.78 minutes 

MG1655: 2310771..2309668
<gbrowseImage> name=NC_000913:2309668..2310771 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2262685..2261750
<gbrowseImage> name=NC_012967:2261750..2262685 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2195473..2196576
<gbrowseImage> name=NC_012759:2195473..2196576 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2316083..2314980
<gbrowseImage> name=NC_007779:2314980..2316083 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2401759..2400656
<gbrowseImage> name=NC_010473:2400656..2401759 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

2309671

Edman degradation

PMID:6297988[2]
PMID:9298646[3]
PMID:9629924[4]


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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

ompC(del) (Keio:JW2203)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC9781[6]

ompC::Tn5KAN-2 (FB20710)

Insertion at nt 469 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20710

contains pKD46

ompC::Tn5KAN-2 (FB20711)

Insertion at nt 469 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20711

does not contain pKD46

ompC171

CGSC:6820

ompC161

CGSC:8752

ompC263

CGSC:9903

ompC264

CGSC:9913

ompC262

CGSC:9918

ompC172

CGSC:14635

ompC768(del)::kan

PMID:16738554[5]

CGSC:102176

ompCp1

protein expression

OmpC protein synthesis is constitutive, less repression in ompCp1 than in wild-type

PMID:7007334[8]

ompC-

insertion

Sensitivity to

Decreased Sensitivity to Micromycin B17

PMID:3543211[9]

See table 4 for full results.

ompC in strain CE104

Resistant to

Resistant to Me1 phage.

PMID:375003[10]

Experimental Strain: CE104

Parental Strain: PC0479


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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

JW2203

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCAAAGTTAAAGTACTGTCCCT

Primer 2:CCGAACTGGTAAACCAGACCCAG

22A6

Kohara Phage

Genobase

PMID:3038334[12]

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[6]

est. P1 cotransduction: 75% [13]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[6]

est. P1 cotransduction: 71% [13]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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

EcoCyc:EG10670

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10670

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000663

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946716

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0664

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007321

Escherichia coli str. K-12 substr. MG1655

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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. ↑ Mizuno, T et al. (1983) DNA sequence of the promoter region of the ompC gene and the amino acid sequence of the signal peptide of pro-OmpC protein of Escherichia coli. FEBS Lett. 151 159-64 PubMed
  3. ↑ 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
  4. ↑ Molloy, MP et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 837-44 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  8. ↑ 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
  9. ↑ Laviña, M et al. (1986) Identification, mapping, cloning and characterization of a gene (sbmA) required for microcin B17 action on Escherichia coli K12. J. Gen. Microbiol. 132 1685-93 PubMed
  10. ↑ Verhoef, C et al. (1979) Genetics and biochemistry of the peptidoglycan-associated proteins b and c of Escherichia coli K12. Mol. Gen. Genet. 169 137-46 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. ↑ 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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