modE:Gene: Difference between revisions

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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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{|   id="I46a9b81b3bdfc"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''modE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''modE''
Molybdenum
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0750, b0761, JW0744, modR, chlD''<ref name='LIB:Riley_2006'/>, chlD''


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!{{table_heading_style}} |Synonyms
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''ECK0750, b0761, JW0744, modR, chlD''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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17.09 minutes&nbsp;
17.09 minutes&nbsp;
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|
MG1655: 793867..793079<br />{{GBrowseFigureByCoord|792079|794867|ecoli|MG1655}}
MG1655: 793867..793079<br /><gbrowseImage>
name=NC_000913:793079..793867
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6395 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6395 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:792079..794867 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|792079|794867|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:793079..793867&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|793079|793867|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6395 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6395 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 775273..774485<br /><gbrowseImage>
name=NC_012967:774485..775273
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|774485|775273|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|774485|775273|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 696047..696835<br /><gbrowseImage>
name=NC_012759:696047..696835
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|696047|696835|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|696047|696835|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 795066..794278<br />{{GBrowseFigureByCoord|793278|796066|ecoli_W3110|W3110}}
W3110: 795066..794278<br /><gbrowseImage>
name=NC_007779:794278..795066
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:793278..796066 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|793278|796066|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:794278..795066&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|794278|795066|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 847795..847007<br /><gbrowseImage>
name=NC_010473:847007..847795
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|845431|849371|GBrowse(DH10B)}}
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===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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!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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&Delta;modE (Keio:JW0744)
&Delta;modE (Keio:JW0744)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107087 CGSC8806]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107087 CGSC8806]<ref name='LIB:cgsc'/>  
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|
modEG133D
|
 
|
G133D
|
 
|
Transcription repression by modE even in the absence of molybdate
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9G8 UniProt:P0A9G8]
|-
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modE
|
 
|
 
|
 
|
 
|
 
|
 
|
Deletion
|-
|
modEA76V
|
 
|
A76V
|
 
|
Partial loss of repression by modE
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9G8 UniProt:P0A9G8]
|-
|
modET125I
|
 
|
T125I
|
 
|
Transcription repression by modE even in the absence of molybdate
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A9G8 UniProt:P0A9G8]
|-
|
''&#916;modE733::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101916|CGSC:101916]]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0744
JW0744
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGCACAGCGTGGCGATAATCAC  
Primer 2:CCGCACAGCGTGGCGATAATCAC  
|-
|-
|
[[:Category:Kohara_Phage:4H1|4H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=179 Genobase]
|
PMID:3038334
|-
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[[:Category:Kohara_Phage:10F3|10F3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=180 Genobase]
|
PMID:3038334
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[[nadA:Gene|nadA57::Tn10]]
[[nadA:Gene|nadA57::Tn10]]
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est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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zbh-29::Tn10
zbh-29::Tn10
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CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10


Synonyms:zbi-29::Tn10
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6395 EcoCyc:G6395] 
EcoCyc:G6395
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3017 EchoBASE:EB3017] 
EcoGene:EG13227
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0761 EcoliGenExpDB:b0761] 
RegulonDB:ECK120002995
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[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=C0837 ECOL199310CYC:C0837]
[http://www.ncbi.nlm.nih.gov/gene?term=945366 GeneID:945366]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13227 EcoGene:EG13227] 
EchoBASE:EB3017
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=MODE ECOO157CYC:MODE] 
ASAP:ABE-0002585
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:mod genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

modE

Mnemonic

Molybdenum

Synonyms

ECK0750, b0761, JW0744, modR, chlD[1], chlD

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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

17.09 minutes 

MG1655: 793867..793079
<gbrowseImage> name=NC_000913:793079..793867 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 775273..774485
<gbrowseImage> name=NC_012967:774485..775273 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 696047..696835
<gbrowseImage> name=NC_012759:696047..696835 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 795066..794278
<gbrowseImage> name=NC_007779:794278..795066 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 847795..847007
<gbrowseImage> name=NC_010473:847007..847795 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

ΔmodE (Keio:JW0744)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8806[3]

modEG133D

G133D

Transcription repression by modE even in the absence of molybdate

seeded from UniProt:P0A9G8

modE

Deletion

modEA76V

A76V

Partial loss of repression by modE

seeded from UniProt:P0A9G8

modET125I

T125I

Transcription repression by modE even in the absence of molybdate

seeded from UniProt:P0A9G8

ΔmodE733::kan

PMID:16738554[2]

CGSC:101916


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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

JW0744

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCAGGCCGAAATCCTTCTCAC

Primer 2:CCGCACAGCGTGGCGATAATCAC

4H1

Kohara Phage

Genobase

PMID:3038334[5]

10F3

Kohara Phage

Genobase

PMID:3038334[5]

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[3]

est. P1 cotransduction: 62% [6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[3]

est. P1 cotransduction: 34% [6]
Synonyms:zbi-29::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:G6395

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002995

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945366

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3017

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002585

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. ↑ 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
  5. ↑ 5.0 5.1 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
  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).

Categories

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