mlaB:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|yrbB}}{{Tab On|Gene|yrbB}}{{Tab|Gene Product(s)|yrbB}}{{Tab|Expression|yrbB}}{{Tab|Evolution|yrbB}}{{Tab|On One Page|yrbB}}{{TabsBottom}}
{{Tab|Quickview|mlaB}}{{Tab On|Gene|mlaB}}{{Tab|Gene Product(s)|mlaB}}{{Tab|Expression|mlaB}}{{Tab|Evolution|mlaB}}{{Tab|On One Page|mlaB}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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="J46a9efd37717f" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yrbB''  
''mlaB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3180, b3191, JW5535''<ref name='LIB:Riley_2006'/>
''ECK3180, b3191, JW5535'', yrbB<ref name='LIB:Riley_2006'/>, JW5535, yrbB''


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*  
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9efd4040f4"  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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71.88 minutes&nbsp;
71.88 minutes&nbsp;
|
|
MG1655: 3335278..3334985<br />{{GBrowseFigureByCoord|3334985|3335278|ecoli|MG1655}}
MG1655: 3335278..3334985<br /><gbrowseImage>
name=NC_000913:3334985..3335278
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7658 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7658 EcoCyc]
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|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 3337111..3336818<br />{{GBrowseFigureByCoord|3336818|3337111|ecoli_W3110|W3110}}
NC_012967: 3272491..3272198<br /><gbrowseImage>
name=NC_012967:3272198..3272491
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3335818|3338111|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|3272198|3272491|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3336818|3337111|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|3272198|3272491|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
 
|
|
NC_012759: 3222133..3222426<br /><gbrowseImage>
name=NC_012759:3222133..3222426
source=BW2952
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 3433023..3432730<br />{{GBrowseFigureByCoord|3432730|3433023|ecoli_DH10B|DH10B}}
{{GBrowseLink|BW2952|012759|3222133|NC_3222426|GBrowse (BW2952)}}
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3432144|3433609|GBrowse(DH10B)}}
{{GBrowseFastaLink|BW2952|012759|3222133|NC_3222426|FASTA Dump}}
|-
|
W3110
|
&nbsp;
|
W3110: 3337111..3336818<br /><gbrowseImage>
name=NC_007779:3336818..3337111
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|3335818|3338111|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3432144|3433609|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3336818|3337111|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 3272198..3272491<br />{{GBrowseFigureByCoord|3272198|3272491|REL606|NC_012967}}
DH10B: 3433023..3432730<br /><gbrowseImage>
name=NC_010473:3432730..3433023
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|3272198|3272491|GBrowse (REL606)}}
{{GBrowseLink|ecoli_DH10B|NC_010473|3432144|3433609|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|3272198|3272491|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3432144|3433609|FASTA Dump}}  


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{|   id="J46a9efd4b7e8e" 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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{|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="X46a9efd50c74f"  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
|-
|
''mlaC(del)''
|


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|
Growth Phenotype
|
Increase outer membrane permeability.
|
PMID:19383799
|
 
|
Figure 1 and 3. 
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16935.A4e04bf5244d21-->
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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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{|   id="L46a9efd5c01fe" class=" tableEdit Gene_resource_table"   
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Primer 2:CCACGAGGCAGAACATCAGCAGG  
Primer 2:CCACGAGGCAGAACATCAGCAGG  
|-
|
[[: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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Synonyms:zha-6::Tn10  
Synonyms:zha-6::Tn10  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|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=G7658 EcoCyc:G7658]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3191 EcoliGenExpDB:b3191]
|
|
   
   
|-  
|-  
|
|
[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=EB2649 EchoBASE:EB2649]
[http://BioCyc.org/ECOL199310/new-image?object=C3950 ECOL199310CYC:C3950]
|
|
   
   
|-  
|-  
|
|
[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=b3191 EcoliGenExpDB:b3191]
[http://BioCyc.org/ECOO157/new-image?object=YRBB ECOO157CYC:YRBB]
|
|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C3950 ECOL199310CYC:C3950]
|
|
   
   
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12797 EcoGene:EG12797]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7658 ECOCYC:G7658]
|
|
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=YRBB ECOO157CYC:YRBB]
[http://www.ncbi.nlm.nih.gov/gene?term=947954 GeneID:947954]
|
|
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=0010487&formSubmitReturn=1 ASAP:ABE-0010487]
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[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: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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

mlaB

Mnemonic
Synonyms

ECK3180, b3191, JW5535, yrbB[1], JW5535, yrbB

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Notes

Location(s) and DNA Sequence

[back to top]


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

71.88 minutes 

MG1655: 3335278..3334985
<gbrowseImage> name=NC_000913:3334985..3335278 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3272491..3272198
<gbrowseImage> name=NC_012967:3272198..3272491 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3222133..3222426
<gbrowseImage> name=NC_012759:3222133..3222426 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3337111..3336818
<gbrowseImage> name=NC_007779:3336818..3337111 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3433023..3432730
<gbrowseImage> name=NC_010473:3432730..3433023 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

mlaC(del)

Growth Phenotype

Increase outer membrane permeability.

PMID:19383799[2]

Figure 1 and 3.

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Notes

Genetic Interactions

[back to top]



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

JW5535

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAGCGAGTCACTGAGCTGGATgca

Primer 2:CCACGAGGCAGAACATCAGCAGG

14F11

Kohara Phage

Genobase

PMID:3038334[4]

7E3

Kohara Phage

Genobase

PMID:3038334[4]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 89% [6]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[5]

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

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3191

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3950

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YRBB

EcoCyc (EcoliWiki Page)

ECOCYC:G7658

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947954

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. ↑ 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
  3. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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