mlaC:Gene: Difference between revisions

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>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3273126..3272491 <gbrowseImage> name=NC_012967:3272491..3273126 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3222426..3223061 <gbrowseImage> name=NC_012759:3222426..3223061 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3337746..3337111 <gbrowseImage> name=NC_007779:3337111..3337746 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3433658..3433023 <gbrowseImage> name=NC_010473:3433023..3433658 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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
↑ ^3.0 ^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
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ 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
↑ ^6.0 ^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
↑ ^7.0 ^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).

mlaC:Gene: Difference between revisions

Latest revision as of 20:46, 19 September 2013

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

@@ Line 9: / Line 9: @@
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 <noinclude>{{TabsTop}}
-{{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}}
 {|
 |- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
 |{{Sub}}[[#Nomenclature |Nomenclature]]
 |{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
+|{{Sub}}[[#Sequence Features|Sequence Features]]
 |{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
+|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
 |{{Sub}}[[#Genetic Resources  |Genetic Resources]]
 |{{Sub}}[[#Accessions in Other Databases |Accessions]]
@@ Line 31: / Line 33: @@
 *
 ****************************************************************************************** -->{{Gene_nomenclature_help}}
-{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{|   id="Q46a9efd9ad263"  class=" tableEdit Gene_nomenclature_table"
 |-
 !align=left {{table_heading_style}} |Standard name
 ||
-''yrbC''
+''mlaC''
 |-
 !align=left {{table_heading_style}} |Mnemonic
@@ Line 44: / Line 46: @@
 !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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 <!--box uid=421aa90e079fa326b6494f812ad13e79.16937.Q46a9efd9ad263-->
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 ****************************************************************************************** -->{{Gene_location_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{| 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"
 |- {{table_heading_style}}
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@@ Line 74: / Line 76: @@
 .89 minutes&nbsp;
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-MG1655: 3335913..3335278<br />{{GBrowseFigureByCoord|3334278|3336913|ecoli|MG1655}}
+MG1655: 3335913..3335278<br /><gbrowseImage>
+name=NC_000913:3335278..3335913
+source=MG1655
+preset=GeneLocation
+</gbrowseImage>
 |
 *[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7659 EcoCyc]
@@ Line 82: / Line 89: @@
 {{GBrowseFastaLink|ecoli|NC_000913|3335278|3335913|FASTA Dump}}
 *[http://biocyc.org/ECOLI/sequence?object=G7659 EcoCyc Sequence Dump]
+|-
+|
+[[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)}}
+|
+{{GBrowseFastaLink|REL606|NC_012967|3272491|3273126|FASTA Dump}}
+|-
+|
+[[BW2952]]
+|
+|
+NC_012759: 3222426..3223061<br /><gbrowseImage>
+name=NC_012759:3222426..3223061
+source=BW2952
+preset=GeneLocation
+</gbrowseImage>
+|
+{{GBrowseLink|BW2952|012759|3222426|NC_3223061|GBrowse (BW2952)}}
+|
+{{GBrowseFastaLink|BW2952|012759|3222426|NC_3223061|FASTA Dump}}
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@@ Line 88: / Line 127: @@
 &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|AC_000091|3336111|3338746|GBrowse(W3110)}}
+{{GBrowseLink|ecoli_W3110|NC_007779|3336111|3338746|GBrowse(W3110)}}
 |
-{{GBrowseFastaLink|ecoli_W3110|AC_000091|3337111|3337746|FASTA Dump}}
+{{GBrowseFastaLink|ecoli_W3110|NC_007779|3337111|3337746|FASTA Dump}}
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@@ Line 99: / Line 143: @@
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-DH10B: 3433658..3433023<br />{{GBrowseFigureByCoord|3431753|3434928|ecoli_DH10B|DH10B}}
+DH10B: 3433658..3433023<br /><gbrowseImage>
+name=NC_010473:3433023..3433658
+source=DH10B
+preset=GeneLocation
+</gbrowseImage>
 |
 {{GBrowseLink|ecoli_DH10B|NC_010473|3431753|3434928|GBrowse(DH10B)}}
@@ Line 105: / Line 154: @@
 {{GBrowseFastaLink|ecoli_DH10B|NC_010473|3431753|3434928|FASTA Dump}}
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+|- class="tableEdit_footer"
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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;"
+{|   id="L46a9efdaed168"  class=" tableEdit Gene_sequence_features_table"
 |- {{table_heading_style}}
-!|Feature type!!Location!!Description
+!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
-|-class='sortbottom'
+|- class="tableEdit_footer"
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+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16937.L46a9efdaed168&page=16937&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.16937.L46a9efdaed168-->
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 ****************************************************************************************** -->{{Gene_alleles_help}}
-{|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="U46a9efdb4159c"  class=" tableEdit Gene_allele_table dataTable"
 |- {{table_heading_style}}
 !|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
+|-
+|
+''&#916;yrbC722::kan''
+|
+|
+|
+|
+|
+PMID:16738554
+|
+[[cgscmutation:106044|CGSC:106044]]
+|
+|-
+|
+''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.
 |-
 |
@@ Line 167: / Line 252: @@
 |-
 |
-''&#916;yrbC722::kan''
+''mlaC(del)'' ''pldA''
 |
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+Growth Phenotype
 |
+Increase outer membrane permeability. Increase was more than single gene mutations.
 |
-PMID:16738554
+PMID:19383799
 |
-[[cgscmutation:106044|CGSC:106044]]
+Parental Strain: JCM158, a deriv in the Keo collection.
+Experimental Strain: JCM736
 |
+Figure 1 and 3.
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16937.U46a9efdb4159c&page=16937&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16937.U46a9efdb4159c&page=16937&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
 |}
 <!--box uid=421aa90e079fa326b6494f812ad13e79.16937.U46a9efdb4159c-->
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 ===Notes===
+==Genetic Interactions==
+{{BacktoTop}}
+<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16937.Y4e04bf53524a0-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
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+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y4e04bf53524a0"  class=" tableEdit Genetic_interaction_table dataTable"
+|- {{table_heading_style}}
+!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.16937.Y4e04bf53524a0&page=16937&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
+|}
+<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16937.Y4e04bf53524a0--></protect>
+<!-- Genetic Interacdtions Notes -->
+===Notes===
 ==Genetic Resources==
@@ Line 201: / Line 310: @@
 *
 ****************************************************************************************** -->{{Gene_resources_help}}
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{|   id="L46a9efdc00242"  class=" tableEdit Gene_resource_table"
 |- {{table_heading_style}}
 !|Resource!!Resource Type!!Source!!Notes/Reference
@@ Line 219: / Line 328: @@
 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
 |-
 |
@@ Line 240: / Line 367: @@
 Synonyms:zha-6::Tn10
-|-class='sortbottom'
+|- class="tableEdit_footer"
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 |}
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 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
 |-
 |
-[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=G7659 EcoCyc:G7659]
+[http://chase.ou.edu/macro/searchlink.php?bnum=b3192 EcoliGenExpDB:b3192]
 |
 |-
 |
-[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
+[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
 |
-[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2650 EchoBASE:EB2650]
+[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
 |
 |-
 |
-[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]
-|
-|-
-|
-[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
-|
-[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
 |
 |-
 |
-[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
+[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
 |
-[http://ecogene.org/geneinfo.php?eg_id=EG12798 EcoGene:EG12798]
+[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7659 ECOCYC:G7659]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
 |
-[http://BioCyc.org/ECOO157/new-image?object=YRBC ECOO157CYC:YRBC]
+[http://www.ncbi.nlm.nih.gov/gene?term=947710 GeneID:947710]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
+[[RegulonDB]]
 |
-[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010489&formSubmitReturn=1 ASAP:ABE-0010489]
+RegulonDB:
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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 [[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]]

mlaC:Gene: Difference between revisions

Latest revision as of 20:46, 19 September 2013

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

References

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