envC:Gene: Difference between revisions

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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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{| id="P46a9fa63a9ffd"  class=" tableEdit Gene_nomenclature_table"   
{|   id="P46a9fa63a9ffd"  class=" tableEdit Gene_nomenclature_table"   


|-
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3603, b3613, JW5646, yibP, slm11''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3603, b3613, JW5646, yibP, slm11''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, slm11''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="M46a9fa6437264"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9fa6437264"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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81.58 minutes&nbsp;
81.58 minutes&nbsp;
|
|
MG1655: 3784861..3786120<br />{{GBrowseFigureByCoord|3784861|3786120|ecoli|MG1655}}
MG1655: 3784861..3786120<br /><gbrowseImage>
name=NC_000913:3784861..3786120
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12297 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12297 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3783861|3787120|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3783861|3787120|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3784861|3786120|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3784861|3786120|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12297 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12297 EcoCyc Sequence Dump]  
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|
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NC_012967: 3727604..3728863<br />{{GBrowseFigureByCoord|3727604|3728863|REL606|NC_012967}}
NC_012967: 3727604..3728863<br /><gbrowseImage>
name=NC_012967:3727604..3728863
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|REL606|NC_012967|3727604|3728863|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3727604|3728863|GBrowse (REL606)}}
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W3110
[[BW2952]]
|
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&nbsp;
 
|
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W3110: 3853577..3852318<br />{{GBrowseFigureByCoord|3852318|3853577|ecoli_W3110|W3110}}
NC_012759: 3673187..3674446<br /><gbrowseImage>
name=NC_012759:3673187..3674446
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3851318|3854577|GBrowse(W3110)}}  
{{GBrowseLink|BW2952|NC_012759|3673187|3674446|GBrowse (BW2952)}}
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3852318|3853577|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3673187|3674446|FASTA Dump}}  
|-  
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[[DH10B]]
W3110
|
&nbsp;
|
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W3110: 3853577..3852318<br /><gbrowseImage>
name=NC_007779:3852318..3853577
source=W3110
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 3882438..3883697<br />{{GBrowseFigureByCoord|3882438|3883697|ecoli_DH10B|DH10B}}
{{GBrowseLink|W3110|NC_007779|3851318|3854577|GBrowse(W3110)}}  
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3879920|3886215|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3879920|3886215|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3852318|3853577|FASTA Dump}}  
|-  
|-  
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[[BW2952]]
[[DH10B]]
|
|


|
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NC_012759: 3673187..3674446<br />{{GBrowseFigureByCoord|3673187|3674446|BW2952|NC_012759}}
DH10B: 3882438..3883697<br /><gbrowseImage>
name=NC_010473:3882438..3883697
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|BW2952|012759|3673187|NC_3674446|GBrowse (BW2952)}}
{{GBrowseLink|DH10B|NC_010473|3879920|3886215|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|BW2952|012759|3673187|NC_3674446|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3879920|3886215|FASTA Dump}}  


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{|   id="T46a9fa64ee169"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9fa64ee169"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17781.T46a9fa64ee169&page=17781&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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*  
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{| {{Prettytable}} id="B46a9fa6543448"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="B46a9fa6543448"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011820 yibP]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011820 yibP::Tn5KAN-2] (FB21343)
|
Insertion at nt 1087 in Plus orientation
|
|


|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21343]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011820 yibP::Tn5KAN-2] (FB21344)
|
Insertion at nt 1087 in Plus orientation
|
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|
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PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21344]
|
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At position 1087 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB21343
contains [[pKD46]]  
|-  
|-  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011820 yibP]
&Delta;yibP::kan
|
deletion
|
|


|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
|


|
|-
|
&Delta;yibP::kan
|
deletion
|
|


|
|
 
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Asparagine]]
|
|
PMID:12519969
PMID:16095938
|
|
[[asapstrains:ASAP|ASAP]]
 
|
|
At position 1087 in Plus orientation, contains plasmid [[pKD46]].<br />ASAP strain name: FB21344
   
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&Delta;yibP::kan
envC
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deletion
deletion
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[[Biolog]]:respiration
Sensitivity to
|
|
unable to respire [[Carbon sources|Acetate]]
increases sensitivity to bicyclomycin
|
|
PMID:16095938
PMID:21357484
|
|


|
|
fig 2


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===Notes===
===Notes===
In ''envC'' mutants, constriction of the OM lags behind the IM and the FtsZ ring.
In ''envC'' mutants, constriction of the OM lags behind the IM and the FtsZ ring.
==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17781.J4e04ba6b51327-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04ba6b51327"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="D46a9fa6605d87"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9fa6605d87"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTCTTCCCAACCACGGCTGTGG  
Primer 2:CCTCTTCCCAACCACGGCTGTGG  
|-
|
[[:Category:Kohara_Phage:16B11|16B11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=574 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5D2|5D2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=575 Genobase]
|
PMID:3038334
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{|   id="A46a9fa66a3db0"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9fa66a3db0"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12297 EcoCyc:EG12297]
EcoCyc:EG12297
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2205 EchoBASE:EB2205]
EcoGene:EG12297
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3613 EcoliGenExpDB:b3613]
RegulonDB:ECK120002178
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4439 ECOL199310CYC:C4439]
[http://www.ncbi.nlm.nih.gov/gene?term=948129 GeneID:948129]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12297 EcoGene:EG12297]
EchoBASE:EB2205
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
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[http://BioCyc.org/ECOO157/new-image?object=YIBP ECOO157CYC:YIBP]
ASAP:ABE-0011820
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011820&formSubmitReturn=1 ASAP:ABE-0011820]
|


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:48, 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

envC

Mnemonic

Envelope

Synonyms

ECK3603, b3613, JW5646, yibP, slm11[1][2], slm11

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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

81.58 minutes 

MG1655: 3784861..3786120
<gbrowseImage> name=NC_000913:3784861..3786120 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3727604..3728863
<gbrowseImage> name=NC_012967:3727604..3728863 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3673187..3674446
<gbrowseImage> name=NC_012759:3673187..3674446 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3853577..3852318
<gbrowseImage> name=NC_007779:3852318..3853577 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3882438..3883697
<gbrowseImage> name=NC_010473:3882438..3883697 source=DH10B preset=GeneLocation </gbrowseImage>

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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
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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

ΔenvC (Keio:JW5646)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11498[4]

yibP::Tn5KAN-2 (FB21343)

Insertion at nt 1087 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB21343

does not contain pKD46

yibP::Tn5KAN-2 (FB21344)

Insertion at nt 1087 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB21344

contains pKD46

ΔyibP::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[6]

ΔyibP::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[6]

envC61

CGSC:11209

ΔenvC725::kan

PMID:16738554[3]

CGSC:100720

ΔenvC

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔnlpD

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔyebA

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔygeR

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔnlpD ΔyebA

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔnlpD ΔygeR

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔyebA ΔygeR

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

ΔenvC ΔyebA ΔygeR ΔnlpD

deletion

deletion

Cell Shape

Defect in Cell Separation

PMID:19525345[7]

envC

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[8]

fig 2

edit table


Notes

In envC mutants, constriction of the OM lags behind the IM and the FtsZ ring.


Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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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

JW5646

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCACACGtGCCGTGAAACCGCG

Primer 2:CCTCTTCCCAACCACGGCTGTGG

16B11

Kohara Phage

Genobase

PMID:3038334[10]

5D2

Kohara Phage

Genobase

PMID:3038334[10]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: % [11]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: 16% [11]

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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

EcoCyc:EG12297

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12297

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002178

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948129

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2205

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011820

Escherichia coli str. K-12 substr. MG1655

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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. ↑ 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 Uehara, T et al. (2009) LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli. J. Bacteriol. 191 5094-107 PubMed
  8. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 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
  11. ↑ 11.0 11.1 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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