emrA:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|emrA}}{{Tab On|Gene|emrA}}{{Tab|Gene Product(s)|emrA}}{{Tab|Expression|emrA}}{{Tab|Evolution|emrA}}{{Tab|On One Page|emrA}}{{TabsBottom}}
{{Tab|Quickview|emrA}}{{Tab On|Gene|emrA}}{{Tab|Gene Product(s)|emrA}}{{Tab|Expression|emrA}}{{Tab|Evolution|emrA}}{{Tab|On One Page|emrA}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''emrA''  
''emrA''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Efflux-multidrug resistance
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2679, b2685, JW2660''<ref name='LIB:Riley_2006'/>, JW2660''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15933.U46a9e3ba7f528&page=15933&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2679, b2685, JW2660''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9e3bb0a365"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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60.55 minutes&nbsp;
60.55 minutes&nbsp;
|
|
MG1655: 2809449..2810621<br />{{GBrowseFigureByCoord|2808449|2811621|ecoli|MG1655}}
MG1655: 2809449..2810621<br /><gbrowseImage>
name=NC_000913:2809449..2810621
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11354 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11354 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2808449..2811621 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2808449|2811621|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2809449..2810621&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2809449|2810621|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11354 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11354 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2706286..2707458<br /><gbrowseImage>
name=NC_012967:2706286..2707458
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2706286|2707458|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2706286|2707458|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2695261..2696433<br /><gbrowseImage>
name=NC_012759:2695261..2696433
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2695261|2696433|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2695261|2696433|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2810083..2811255<br />{{GBrowseFigureByCoord|2809083|2812255|ecoli_W3110|W3110}}  
W3110: 2810083..2811255<br /><gbrowseImage>
name=NC_007779:2810083..2811255
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2809083|2812255|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2810083|2811255|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2809083..2812255 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2810083..2811255&plugin_action=Go FASTA Dump]
 
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DH10B: 2901991..2903163<br /><gbrowseImage>
name=NC_010473:2901991..2903163
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2899647|2905507|GBrowse(DH10B)}}
|
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e3bc0b119"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;emrA (Keio:JW2660)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108379 CGSC10098]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;emrA766::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100698|CGSC:100698]]
|
|-  
|
pEMR2.1 in strain RP437
|
 
|
 
|
Resistant to
|
This milticopy plasmid in strain RP437, ''emrA'' <sup>  +</sup> & ''emrB'' <sup>  +</sup>  in pUC18, is resistant to Nalidixic acid
|
PMID:1409590
|
Parental: RP437 [http://cgsc.biology.yale.edu/Strain.php?ID=111960 CGSC]
 
Expiramental: RP437 with plasmid pEMR2.1
|
|-
|
pEMR2.1 in strain RP437
|
 
|
 
|
Resistant to
|
This milticopy plasmid in strain RP437, ''emrA'' <sup>  +</sup> & ''emrB'' <sup>  +</sup>  in pUC18, is resistant to Carbonyl cyanide m-chlorophenyl hydrazone (CCCP).
|
PMID:1409590
|
Parental: RP437 [http://cgsc.biology.yale.edu/Strain.php?ID=111960 CGSC]
 
Expiramental: RP437 with plasmid pEMR2.1
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2660
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAGCGCAAATGCGGAGACTCA
 
Primer 2:CCGCCAGCGTTAGCTTTTACGAT
|-
|
[[:Category:Kohara_Phage:8G10|8G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=445 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:23B7|23B7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=446 Genobase]
|
PMID:3038334
|-
|
[[pheA:Gene|pheA18::Tn10]]
|
Linked marker
|
CAG12158 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40091 CGSC7421]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[srlD:Gene|srlD3131::Tn10]]
|
Linked marker
|
CAG18642 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40097 CGSC7423]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 56% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
 
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11354 EcoCyc:EG11354] 
EcoCyc:EG11354
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1329 EchoBASE:EB1329] 
EcoGene:EG11354
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2685 EcoliGenExpDB:b2685] 
RegulonDB:ECK120001323
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=C3238 ECOL199310CYC:C3238]
[http://www.ncbi.nlm.nih.gov/gene?term=947166 GeneID:947166]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11354 EcoGene:EG11354] 
EchoBASE:EB1329
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=EMRA ECOO157CYC:EMRA] 
ASAP:ABE-0008838
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33259 CGSC:33259] 
|
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:emr genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

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

Standard name

emrA

Mnemonic

Efflux-multidrug resistance

Synonyms

ECK2679, b2685, JW2660[1], JW2660

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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

60.55 minutes 

MG1655: 2809449..2810621
<gbrowseImage> name=NC_000913:2809449..2810621 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2706286..2707458
<gbrowseImage> name=NC_012967:2706286..2707458 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2695261..2696433
<gbrowseImage> name=NC_012759:2695261..2696433 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2810083..2811255
<gbrowseImage> name=NC_007779:2810083..2811255 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2901991..2903163
<gbrowseImage> name=NC_010473:2901991..2903163 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

ΔemrA (Keio:JW2660)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10098[3]

ΔemrA766::kan

PMID:16738554[2]

CGSC:100698

pEMR2.1 in strain RP437

Resistant to

This milticopy plasmid in strain RP437, emrA + & emrB + in pUC18, is resistant to Nalidixic acid

PMID:1409590[4]

Parental: RP437 CGSC

Expiramental: RP437 with plasmid pEMR2.1

pEMR2.1 in strain RP437

Resistant to

This milticopy plasmid in strain RP437, emrA + & emrB + in pUC18, is resistant to Carbonyl cyanide m-chlorophenyl hydrazone (CCCP).

PMID:1409590[4]

Parental: RP437 CGSC

Expiramental: RP437 with plasmid pEMR2.1


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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

JW2660

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGCGCAAATGCGGAGACTCA

Primer 2:CCGCCAGCGTTAGCTTTTACGAT

8G10

Kohara Phage

Genobase

PMID:3038334[6]

23B7

Kohara Phage

Genobase

PMID:3038334[6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[3]

est. P1 cotransduction: 1% [7]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[3]

est. P1 cotransduction: 56% [7]
Synonyms:zfh-3131::Tn10, zfi-3131::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

EcoCyc

EcoCyc:EG11354

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11354

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001323

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947166

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1329

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008838

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. ↑ 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. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Lomovskaya, O & Lewis, K (1992) Emr, an Escherichia coli locus for multidrug resistance. Proc. Natl. Acad. Sci. U.S.A. 89 8938-42 PubMed
  5. ↑ 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. ↑ 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. ↑ 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).

Categories

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