mlaD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|yrbD}}{{Tab On|Gene|yrbD}}{{Tab|Gene Product(s)|yrbD}}{{Tab|Expression|yrbD}}{{Tab|Evolution|yrbD}}{{Tab|On One Page|yrbD}}{{TabsBottom}}
{{Tab|Quickview|mlaD}}{{Tab On|Gene|mlaD}}{{Tab|Gene Product(s)|mlaD}}{{Tab|Expression|mlaD}}{{Tab|Evolution|mlaD}}{{Tab|On One Page|mlaD}}{{TabsBottom}}
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|- 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="J46a9efdfe38b3" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yrbD''  
''mlaD''
|-
|-
!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
||
||
''ECK3182, b3193, JW3160, vpsC(S.f.)''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3182, b3193, JW3160, vpsC(S.f.)'', yrbD<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, vpsC, yrbD''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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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="V46a9efe06f932"  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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71.9 minutes&nbsp;
71.9 minutes&nbsp;
|
|
MG1655: 3336483..3335932<br />{{GBrowseFigureByCoord|3335932|3336483|ecoli|MG1655}}
MG1655: 3336483..3335932<br /><gbrowseImage>
name=NC_000913:3335932..3336483
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12799 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12799 EcoCyc]
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{{GBrowseFastaLink|ecoli|NC_000913|3335932|3336483|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|3335932|3336483|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12799 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12799 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 3273696..3273145<br /><gbrowseImage>
name=NC_012967:3273145..3273696
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|3273145|3273696|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3273145|3273696|FASTA Dump}}
|-
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[[BW2952]]
|
|
NC_012759: 3223080..3223631<br /><gbrowseImage>
name=NC_012759:3223080..3223631
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|012759|3223080|NC_3223631|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3223080|NC_3223631|FASTA Dump}}
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&nbsp;
&nbsp;
|
|
W3110: 3338316..3337765<br />{{GBrowseFigureByCoord|3337765|3338316|ecoli_W3110|W3110}}
W3110: 3338316..3337765<br /><gbrowseImage>
name=NC_007779:3337765..3338316
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3336765|3339316|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|3336765|3339316|GBrowse(W3110)}}  
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3337765|3338316|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3337765|3338316|FASTA Dump}}  
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|
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DH10B: 3434228..3433677<br />{{GBrowseFigureByCoord|3433677|3434228|ecoli_DH10B|DH10B}}
DH10B: 3434228..3433677<br /><gbrowseImage>
name=NC_010473:3433677..3434228
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3432575|3435330|GBrowse(DH10B)}}
{{GBrowseLink|ecoli_DH10B|NC_010473|3432575|3435330|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3432575|3435330|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3432575|3435330|FASTA Dump}}  


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{|   id="R46a9efe12eab4" 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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****************************************************************************************** -->{{Gene_alleles_help}}
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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="K46a9efe176ccd"  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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|-
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''mlaE(del)''
|
|
|
Growth Phenotype
|
Increase outer membrane permeability.
|
PMID:19383799
|
Parental Strain: JCM158, A derivative of the Keo Collection.


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Experimental Strain: JCM529
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Figure 1 and 3.
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16939.K4e04bf5460c1e-->
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|- {{table_heading_style}}
!|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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Primer 2:CCTTTCGTTGTACCCACAGGTTC  
Primer 2:CCTTTCGTTGTACCCACAGGTTC  
|-
|
[[: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=EG12799 EcoCyc:EG12799]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3193 EcoliGenExpDB:b3193]
|
|
   
   
|-  
|-  
|
|
[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=EB2651 EchoBASE:EB2651]
[http://BioCyc.org/ECOL199310/new-image?object=C3953 ECOL199310CYC:C3953]
|
|
   
   
|-  
|-  
|
|
[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=b3193 EcoliGenExpDB:b3193]
[http://BioCyc.org/ECOO157/new-image?object=YRBD ECOO157CYC:YRBD]
|
|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C3953 ECOL199310CYC:C3953]
|
|
   
   
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12799 EcoGene:EG12799]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12799 ECOCYC:EG12799]
|
|
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=YRBD ECOO157CYC:YRBD]
[http://www.ncbi.nlm.nih.gov/gene?term=947712 GeneID:947712]
|
|
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=0010493&formSubmitReturn=1 ASAP:ABE-0010493]
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

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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

[back to top]


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

Standard name

mlaD

Mnemonic
Synonyms

ECK3182, b3193, JW3160, vpsC(S.f.), yrbD[1][2], vpsC, yrbD

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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

71.9 minutes 

MG1655: 3336483..3335932
<gbrowseImage> name=NC_000913:3335932..3336483 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3273696..3273145
<gbrowseImage> name=NC_012967:3273145..3273696 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3223080..3223631
<gbrowseImage> name=NC_012759:3223080..3223631 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3338316..3337765
<gbrowseImage> name=NC_007779:3337765..3338316 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3434228..3433677
<gbrowseImage> name=NC_010473:3433677..3434228 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

ΔyrbD (Keio:JW3160)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10398[4]

ΔyrbD723::kan

PMID:16738554[3]

CGSC:106046

mlaE(del)

Growth Phenotype

Increase outer membrane permeability.

PMID:19383799[5]

Parental Strain: JCM158, A derivative of the Keo Collection.

Experimental Strain: JCM529

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

JW3160

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCAAACGAAAAAAAATGAAAT

Primer 2:CCTTTCGTTGTACCCACAGGTTC

14F11

Kohara Phage

Genobase

PMID:3038334[7]

7E3

Kohara Phage

Genobase

PMID:3038334[7]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[4]

est. P1 cotransduction: 86% [8]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[4]

est. P1 cotransduction: 34% [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:b3193

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3953

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YRBD

EcoCyc (EcoliWiki Page)

ECOCYC:EG12799

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947712

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. ↑ 7.0 7.1 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
  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).

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