mlaD:Gene: Difference between revisions

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{|   id="V46a9efe06f932"  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="V46a9efe06f932"  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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W3110: 3338316..3337765<br /><gbrowseImage>
W3110: 3338316..3337765<br /><gbrowseImage>
name=AC_000091:3337765..3338316
name=NC_007779:3337765..3338316
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{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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{|   id="K4e04bf5460c1e"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K4e04bf5460c1e"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="E46a9efe2d0f40"  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="E46a9efe2d0f40"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12799 EcoCyc:EG12799]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2651 EchoBASE:EB2651]
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[http://BioCyc.org/ECOL199310/new-image?object=C3953 ECOL199310CYC:C3953]
[http://BioCyc.org/ECOL199310/new-image?object=C3953 ECOL199310CYC:C3953]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12799 EcoGene:EG12799]
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[http://BioCyc.org/ECOO157/new-image?object=YRBD ECOO157CYC:YRBD]
[http://BioCyc.org/ECOO157/new-image?object=YRBD ECOO157CYC:YRBD]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010493&formSubmitReturn=1 ASAP:ABE-0010493]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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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

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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

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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

71.9 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

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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

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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<protect>

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).

Categories

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