yijD: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="Y46aa037554ea1"  class=" tableEdit Gene_nomenclature_table"   
{|   id="Y46aa037554ea1"  class=" tableEdit Gene_nomenclature_table"   


|-
|-
!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yijD''  
''yijD''
|-
|-
!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Systematic nomenclature
|-
|-
!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
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''ECK3956, b3964, JW3936''<ref name='LIB:Riley_2006'/>
''ECK3956, b3964, JW3936''<ref name='LIB:Riley_2006'/>, JW3936''


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{|   id="Q46aa0375d7858"  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="Q46aa0375d7858"  class=" tableEdit Gene_location_table"   
|-
|- {{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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89.66 minutes, 89.66 minutes&nbsp;
89.66 minutes, 89.66 minutes&nbsp;
|
|
MG1655: 4159794..4160153<br />{{GBrowseFigureByCoord|4159794|4160153|ecoli|MG1655}}
MG1655: 4159794..4160153<br /><gbrowseImage>
name=NC_000913:4159794..4160153
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11395 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11395 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4158794|4161153|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4158794|4161153|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|4159794|4160153|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4159794|4160153|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11395 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11395 EcoCyc Sequence Dump]  
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|
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NC_012967: 4141632..4141991<br />{{GBrowseFigureByCoord|4141632|4141991|REL606|NC_012967}}
NC_012967: 4141632..4141991<br /><gbrowseImage>
name=NC_012967:4141632..4141991
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|4141632|4141991|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|4141632|4141991|GBrowse (REL606)}}
|
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{{GBrowseFastaLink|REL606|NC_012967|4141632|4141991|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|4141632|4141991|FASTA Dump}}  
|-
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[[BW2952]]
|
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NC_012759: 4049463..4049822<br /><gbrowseImage>
name=NC_012759:4049463..4049822
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|4049463|4049822|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|4049463|4049822|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 3474910..3474551<br />{{GBrowseFigureByCoord|3474551|3474910|ecoli_W3110|W3110}}
W3110: 3474910..3474551<br /><gbrowseImage>
name=NC_007779:3474551..3474910
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3473551|3475910|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3473551|3475910|GBrowse(W3110)}}  
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3474551|3474910|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3474551|3474910|FASTA Dump}}  
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|
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DH10B: 4259491..4259850<br />{{GBrowseFigureByCoord|4259491|4259850|ecoli_DH10B|DH10B}}
DH10B: 4259491..4259850<br /><gbrowseImage>
name=NC_010473:4259491..4259850
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|4258773|4260568|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4258773|4260568|GBrowse(DH10B)}}
|
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4258773|4260568|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4258773|4260568|FASTA Dump}}  


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{|   id="O46aa03769d9da"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aa03769d9da"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18487.O46aa03769d9da&page=18487&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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{|   id="M46aa0376e87e6"  class=" tableEdit Gene_allele_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa0376e87e6"  class=" tableEdit Gene_allele_table dataTable"   
|-
|- {{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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18487.D4e04cb17ab4bd-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D4e04cb17ab4bd"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18487.D4e04cb17ab4bd&page=18487&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18487.D4e04cb17ab4bd--></protect>
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="P46aa0377ae725"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46aa0377ae725"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCtTCAGCAACTTCCTGCTTACG  
Primer 2:CCtTCAGCAACTTCCTGCTTACG  
|-
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[[:Category:Kohara_Phage:4G11|4G11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=535 Genobase]
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PMID:3038334
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{|   id="N46aa03785b1cd"  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="N46aa03785b1cd"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|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=EG11395 EcoCyc:EG11395]
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|-
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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=EB1368 EchoBASE:EB1368]
EcoCyc:EG11395
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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]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3964 EcoliGenExpDB:b3964]
EcoGene:EG11395
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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]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C4927 ECOL199310CYC:C4927]
RegulonDB:ECK120001362
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://ecogene.org/geneinfo.php?eg_id=EG11395 EcoGene:EG11395]
[http://www.ncbi.nlm.nih.gov/gene?term=948459 GeneID:948459]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YIJD ECOO157CYC:YIJD]
EchoBASE:EB1368
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012981&formSubmitReturn=1 ASAP:ABE-0012981]
ASAP:ABE-0012981
|
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''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:yij genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:yij genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 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

yijD

Mnemonic

Systematic nomenclature

Synonyms

ECK3956, b3964, JW3936[1], JW3936

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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

89.66 minutes, 89.66 minutes 

MG1655: 4159794..4160153
<gbrowseImage> name=NC_000913:4159794..4160153 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4141632..4141991
<gbrowseImage> name=NC_012967:4141632..4141991 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4049463..4049822
<gbrowseImage> name=NC_012759:4049463..4049822 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3474910..3474551
<gbrowseImage> name=NC_007779:3474551..3474910 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4259491..4259850
<gbrowseImage> name=NC_010473:4259491..4259850 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

ΔyijD (Keio:JW3936)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10841[3]

ΔyijD752::kan

PMID:16738554[2]

CGSC:105438


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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

JW3936

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAACAAGCAAATCAAGATAG

Primer 2:CCtTCAGCAACTTCCTGCTTACG

4G11

Kohara Phage

Genobase

PMID:3038334[5]

argE86::Tn10

Linked marker

CAG12185 = CGSC7471[3]

est. P1 cotransduction: 78% [6]

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[3]

est. P1 cotransduction: 25% [6]
Synonyms:thi-39::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:EG11395

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11395

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001362

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948459

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1368

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012981

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. ↑ 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. ↑ 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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