mlaF:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|yrbF}}{{Tab On|Gene|yrbF}}{{Tab|Gene Product(s)|yrbF}}{{Tab|Expression|yrbF}}{{Tab|Evolution|yrbF}}{{Tab|On One Page|yrbF}}{{TabsBottom}}
{{Tab|Quickview|mlaF}}{{Tab On|Gene|mlaF}}{{Tab|Gene Product(s)|mlaF}}{{Tab|Expression|mlaF}}{{Tab|Evolution|mlaF}}{{Tab|On One Page|mlaF}}{{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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{|{{Prettytable}}
{|  id="Z46a9efec74c5c"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yrbF''  
''mlaF''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3184, b3195, JW3162, vpsA(S.f.)''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3184, b3195, JW3162, vpsA(S.f.)'', yrbF<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, vpsA, yrbF''
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='144030'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9efed00c75"  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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71.93 minutes&nbsp;
71.93 minutes&nbsp;
|
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MG1655: 3338087..3337278<br />{{GBrowseFigureByCoord|3336278|3339087|ecoli|MG1655}}
MG1655: 3338087..3337278<br /><gbrowseImage>
name=NC_000913:3337278..3338087
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12801 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12801 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3336278..3339087 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|3336278|3339087|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3337278..3338087&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|3337278|3338087|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12801 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12801 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 3275300..3274491<br /><gbrowseImage>
name=NC_012967:3274491..3275300
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3274491|3275300|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3274491|3275300|FASTA Dump}}
|-
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[[BW2952]]
|
 
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NC_012759: 3224426..3225235<br /><gbrowseImage>
name=NC_012759:3224426..3225235
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|3224426|NC_3225235|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|3224426|NC_3225235|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3339920..3339111<br />{{GBrowseFigureByCoord|3338111|3340920|ecoli_W3110|W3110}}
W3110: 3339920..3339111<br /><gbrowseImage>
name=NC_007779:3339111..3339920
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3338111..3340920 GBrowse(W3110)]
{{GBrowseLink|ecoli_W3110|NC_007779|3338111|3340920|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3339111..3339920&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3339111|3339920|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3435832..3435023<br /><gbrowseImage>
name=NC_010473:3435023..3435832
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3433405|3437450|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3433405|3437450|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C46a9efee07f61"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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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=108681 CGSC10400]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108681 CGSC10400]<ref name='LIB:cgsc'/>  
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:106050|CGSC:106050]]
[[cgscmutation:106050|CGSC:106050]]
|
|
   
   
|-
|
''mlaF(del)''
|
|
|
Growth Phenotype
|
Increase outer membrane permeability.
|
PMID:19383799
|
Parental Strain: JCM158 a deriv of keo collection.
Experimental Strain: JCM531
|
Figure 1 and 3.


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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16943.Q4e04bf5688e26-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q4e04bf5688e26"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW3162
JW3162
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCACTCCCTGGTAAAAGATCAGC  
Primer 2:CCACTCCCTGGTAAAAGATCAGC  
|-
|-
|
[[: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: 82% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 82% <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: 36% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 36% <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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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12801 EcoCyc:EG12801]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3195 EcoliGenExpDB:b3195]
|
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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=EB2653 EchoBASE:EB2653]
[http://BioCyc.org/ECOL199310/new-image?object=C3955 ECOL199310CYC:C3955]
|
|
   
   
|-
|-  
|
|
[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=b3195 EcoliGenExpDB:b3195]
[http://BioCyc.org/ECOO157/new-image?object=YRBF ECOO157CYC:YRBF]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3955 ECOL199310CYC:C3955]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12801 ECOCYC:EG12801]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[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=EG12801 EcoGene:EG12801]
[http://www.ncbi.nlm.nih.gov/gene?term=947729 GeneID:947729]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YRBF ECOO157CYC:YRBF] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone 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

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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

mlaF

Mnemonic
Synonyms

ECK3184, b3195, JW3162, vpsA(S.f.), yrbF[1][2], vpsA, yrbF

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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

71.93 minutes 

MG1655: 3338087..3337278
<gbrowseImage> name=NC_000913:3337278..3338087 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3275300..3274491
<gbrowseImage> name=NC_012967:3274491..3275300 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3224426..3225235
<gbrowseImage> name=NC_012759:3224426..3225235 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3339920..3339111
<gbrowseImage> name=NC_007779:3339111..3339920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3435832..3435023
<gbrowseImage> name=NC_010473:3435023..3435832 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

ΔyrbF (Keio:JW3162)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10400[4]

ΔyrbF725::kan

PMID:16738554[3]

CGSC:106050

mlaF(del)

Growth Phenotype

Increase outer membrane permeability.

PMID:19383799[5]

Parental Strain: JCM158 a deriv of keo collection.

Experimental Strain: JCM531

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

JW3162

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGAGCAGTCTGTGGCGAATTT

Primer 2:CCACTCCCTGGTAAAAGATCAGC

7E3

Kohara Phage

Genobase

PMID:3038334[7]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[4]

est. P1 cotransduction: 82% [8]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[4]

est. P1 cotransduction: 36% [8]
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:b3195

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3955

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YRBF

EcoCyc (EcoliWiki Page)

ECOCYC:EG12801

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947729

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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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. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 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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