mlaC:Gene: Difference between revisions

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{{Tab|Quickview|yrbC}}{{Tab On|Gene|yrbC}}{{Tab|Gene Product(s)|yrbC}}{{Tab|Expression|yrbC}}{{Tab|Evolution|yrbC}}{{Tab|On One Page|yrbC}}{{TabsBottom}}
{{Tab|Quickview|mlaC}}{{Tab On|Gene|mlaC}}{{Tab|Gene Product(s)|mlaC}}{{Tab|Expression|mlaC}}{{Tab|Evolution|mlaC}}{{Tab|On One Page|mlaC}}{{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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
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[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yrbC''  
''mlaC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3181, b3192, JW3159''<ref name='LIB:Riley_2006'/>
''ECK3181, b3192, JW3159'', yrbC<ref name='LIB:Riley_2006'/>, JW3159, yrbC''
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9efda39700"  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
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MG1655
MG1655
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71.89 minutes&nbsp;
71.89 minutes&nbsp;
|
|
MG1655: 3335913..3335278<br />{{GBrowseFigureByCoord|3334278|3336913|ecoli|MG1655}}
MG1655: 3335913..3335278<br /><gbrowseImage>
name=NC_000913:3335278..3335913
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7659 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7659 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3334278..3336913 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|3334278|3336913|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3335278..3335913&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|3335278|3335913|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7659 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7659 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 3273126..3272491<br /><gbrowseImage>
name=NC_012967:3272491..3273126
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3272491|3273126|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3272491|3273126|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 3222426..3223061<br /><gbrowseImage>
name=NC_012759:3222426..3223061
source=BW2952
preset=GeneLocation
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|
{{GBrowseLink|BW2952|012759|3222426|NC_3223061|GBrowse (BW2952)}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 3337746..3337111<br />{{GBrowseFigureByCoord|3336111|3338746|ecoli_W3110|W3110}}  
W3110: 3337746..3337111<br /><gbrowseImage>
name=NC_007779:3337111..3337746
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|3336111|3338746|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3336111..3338746 GBrowse(W3110)]
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3337111|3337746|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3337111..3337746&plugin_action=Go FASTA Dump]
[[DH10B]]
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DH10B: 3433658..3433023<br /><gbrowseImage>
name=NC_010473:3433023..3433658
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3431753|3434928|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3431753|3434928|FASTA Dump}}
 
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===Notes===
===Notes===
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{|  id="L46a9efdaed168"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9efdb4159c"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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''&#916;yrbC722::kan''
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PMID:16738554
|
[[cgscmutation:106044|CGSC:106044]]
|
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''mlaC(del)''
|
 
|
 
|
Growth Phenotype
|
Increase outer membrane permeability.
|
PMID:19383799
|
Parental Strain: JCM158, a Derivative from the Keo Collection.
 
Experimental Strain: JCM528
|
Figure 1 and 3. 
|-  
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&Delta;yrbC (Keio:JW3159)
&Delta;yrbC (Keio:JW3159)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108678 CGSC10397]<ref name='LIB:cgsc'/>  
|
|-
|
''mlaC(del)'' ''pldA''
|
 
|
 
|
Growth Phenotype
|
Increase outer membrane permeability. Increase was more than single gene mutations.
|
PMID:19383799
|
Parental Strain: JCM158, a deriv in the Keo collection.
 
Experimental Strain: JCM736
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
Figure 1 and 3.
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===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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JW3159
JW3159
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTTTTTCTCTTCCAGAGTGAT  
Primer 2:CCTTTTTTCTCTTCCAGAGTGAT  
|-
|-
|
[[:Category:Kohara_Phage:14F11|14F11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=521 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7E3|7E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=522 Genobase]
|
PMID:3038334
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[[sfsB:Gene|sfsB203::Tn10]]
[[sfsB:Gene|sfsB203::Tn10]]
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CAG12072 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38770 CGSC7440]<ref name='LIB:cgsc'/>
CAG12072 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38770 CGSC7440]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zgj-203::Tn10, zha-203::Tn10  
Synonyms:zgj-203::Tn10, zha-203::Tn10  
|-
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[[yhcF:Gene|zhc-6::Tn10]]
[[yhcF:Gene|zhc-6::Tn10]]
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CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 33% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 33% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zha-6::Tn10


Synonyms:zha-6::Tn10
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9efdc9b36e"  class=" tableEdit Gene_accessions_table" 
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7659 EcoCyc:G7659]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3192 EcoliGenExpDB:b3192]
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|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2650 EchoBASE:EB2650]
[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
|
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|-
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3192 EcoliGenExpDB:b3192]
[http://BioCyc.org/ECOO157/new-image?object=YRBC ECOO157CYC:YRBC]
|
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|-
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7659 ECOCYC:G7659]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12798 EcoGene:EG12798]
[http://www.ncbi.nlm.nih.gov/gene?term=947710 GeneID:947710]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOO157/new-image?object=YRBC ECOO157CYC:YRBC] 
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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:yrb genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 19 September 2013

{{#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

mlaC

Mnemonic
Synonyms

ECK3181, b3192, JW3159, yrbC[1], JW3159, yrbC

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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

71.89 minutes 

MG1655: 3335913..3335278
<gbrowseImage> name=NC_000913:3335278..3335913 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3273126..3272491
<gbrowseImage> name=NC_012967:3272491..3273126 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3222426..3223061
<gbrowseImage> name=NC_012759:3222426..3223061 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3337746..3337111
<gbrowseImage> name=NC_007779:3337111..3337746 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3433658..3433023
<gbrowseImage> name=NC_010473:3433023..3433658 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
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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

ΔyrbC722::kan

PMID:16738554[2]

CGSC:106044

mlaC(del)

Growth Phenotype

Increase outer membrane permeability.

PMID:19383799[3]

Parental Strain: JCM158, a Derivative from the Keo Collection.

Experimental Strain: JCM528

Figure 1 and 3.

ΔyrbC (Keio:JW3159)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10397[4]

mlaC(del) pldA

Growth Phenotype

Increase outer membrane permeability. Increase was more than single gene mutations.

PMID:19383799[3]

Parental Strain: JCM158, a deriv in the Keo collection.

Experimental Strain: JCM736

Figure 1 and 3.

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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

JW3159

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTTAAACGTTTAATGATGGT

Primer 2:CCTTTTTTCTCTTCCAGAGTGAT

14F11

Kohara Phage

Genobase

PMID:3038334[6]

7E3

Kohara Phage

Genobase

PMID:3038334[6]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[4]

est. P1 cotransduction: 88% [7]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[4]

est. P1 cotransduction: 33% [7]
Synonyms:zha-6::Tn10

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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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3192

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3952

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YRBC

EcoCyc (EcoliWiki Page)

ECOCYC:G7659

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947710

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 Malinverni, JC & Silhavy, TJ (2009) An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Proc. Natl. Acad. Sci. U.S.A. 106 8009-14 PubMed
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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

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