php:Gene: Difference between revisions

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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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="N46a9f47505f8d"  class=" tableEdit Gene_nomenclature_table"   
{|   id="N46a9f47505f8d"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3366, b3379, JW3342, yhfV''<ref name='LIB:Riley_2006'/>
''ECK3366, b3379, JW3342, yhfV''<ref name='LIB:Riley_2006'/>, yhfV''


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{|   id="T46a9f47589ace"  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="T46a9f47589ace"  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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75.56 minutes&nbsp;
75.56 minutes&nbsp;
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MG1655: 3506612..3505734<br />{{GBrowseFigureByCoord|3505734|3506612|ecoli|MG1655}}
MG1655: 3506612..3505734<br /><gbrowseImage>
name=NC_000913:3505734..3506612
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7731 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7731 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3504734|3507612|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3504734|3507612|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3505734|3506612|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3505734|3506612|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7731 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7731 EcoCyc Sequence Dump]  
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NC_012967: 3436394..3437272<br />{{GBrowseFigureByCoord|3436394|3437272|REL606|NC_012967}}
NC_012967: 3436394..3437272<br /><gbrowseImage>
name=NC_012967:3436394..3437272
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|3436394|3437272|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3436394|3437272|GBrowse (REL606)}}
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NC_012759: 3392891..3393769<br />{{GBrowseFigureByCoord|3392891|3393769|BW2952|NC_012759}}
NC_012759: 3392891..3393769<br /><gbrowseImage>
name=NC_012759:3392891..3393769
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|3392891|NC_3393769|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3392891|3393769|GBrowse (BW2952)}}
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&nbsp;
&nbsp;
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W3110: 4131826..4132704<br />{{GBrowseFigureByCoord|4131826|4132704|ecoli_W3110|W3110}}
W3110: 4131826..4132704<br /><gbrowseImage>
name=NC_007779:4131826..4132704
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|4130826|4133704|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4130826|4133704|GBrowse(W3110)}}  
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DH10B: 3604357..3603479<br />{{GBrowseFigureByCoord|3603479|3604357|ecoli_DH10B|DH10B}}
DH10B: 3604357..3603479<br /><gbrowseImage>
name=NC_010473:3603479..3604357
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|3601723|3606113|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3601723|3606113|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3601723|3606113|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3601723|3606113|FASTA Dump}}  


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{|   id="U46a9f4764a92f"  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="U46a9f4764a92f"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
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Coding Start (SO:0000323)
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[[MG1655]]
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3505734
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Edman degradation
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PMID:9692977<br />
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{| {{Prettytable}} id="U46a9f4769367c"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46a9f4769367c"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
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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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17307.V4e04c1211375f-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V4e04c1211375f"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.17307.V4e04c1211375f&page=17307&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="J46a9f47753de3"  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="J46a9f47753de3"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTGGAAAAATTGAGAGGGATT  
Primer 2:CCTTGGAAAAATTGAGAGGGATT  
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[[:Category:Kohara_Phage:6F9|6F9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=623 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:15C3|15C3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=624 Genobase]
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PMID:3038334
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{|   id="E46a9f477f0851"  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="E46a9f477f0851"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7731 EcoCyc:G7731]
EcoCyc:G7731
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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=EB2753 EchoBASE:EB2753]
EcoGene:EG12917
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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]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3379 EcoliGenExpDB:b3379]
RegulonDB:ECK120004274
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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]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4149 ECOL199310CYC:C4149]
[http://www.ncbi.nlm.nih.gov/gene?term=947891 GeneID:947891]
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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=EG12917 EcoGene:EG12917]
EchoBASE:EB2753
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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=0011044&formSubmitReturn=1 ASAP:ABE-0011044]
ASAP:ABE-0011044
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:47, 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

php

Mnemonic

Phosphotriesterase homology protein

Synonyms

ECK3366, b3379, JW3342, yhfV[1], yhfV

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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

75.56 minutes 

MG1655: 3506612..3505734
<gbrowseImage> name=NC_000913:3505734..3506612 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3436394..3437272
<gbrowseImage> name=NC_012967:3436394..3437272 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3392891..3393769
<gbrowseImage> name=NC_012759:3392891..3393769 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4131826..4132704
<gbrowseImage> name=NC_007779:4131826..4132704 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3604357..3603479
<gbrowseImage> name=NC_010473:3603479..3604357 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

Coding Start (SO:0000323)

MG1655

3505734

Edman degradation

PMID:9692977[2]


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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

Δphp (Keio:JW3342)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10495[4]

Δphp-786::kan

PMID:16738554[3]

CGSC:102366


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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

JW3342

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGTTTTGATCCGACGGGTTA

Primer 2:CCTTGGAAAAATTGAGAGGGATT

6F9

Kohara Phage

Genobase

PMID:3038334[6]

15C3

Kohara Phage

Genobase

PMID:3038334[6]

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[4]

est. P1 cotransduction: 91% [7]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[4]

est. P1 cotransduction: 5% [7]
Synonyms:zhg-3086::Tn10, zhh-21::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:G7731

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12917

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004274

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947891

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2753

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011044

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. ↑ Buchbinder, JL et al. (1998) Biochemical Characterization and Crystallographic Structure of an Escherichia coli Protein from the Phosphotriesterase Gene Family. Biochemistry 37 10860 PubMed
  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. ↑ 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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