atpG: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="J46a9fd870bb5e"  class=" tableEdit Gene_nomenclature_table"   


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{|   id="Y46a9fd878e67d"  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="Y46a9fd878e67d"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{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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84.39 minutes, 84.39 minutes 
84.39 minutes, 84.39 minutes 
|
|
MG1655: 3916288..3915425<br />{{GBrowseFigureByCoord|3915425|3916288|ecoli|MG1655}}
MG1655: 3916288..3915425<br /><gbrowseImage>
name=NC_000913:3915425..3916288
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10104 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10104 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3914425|3917288|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3914425|3917288|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3915425|3916288|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3915425|3916288|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10104 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10104 EcoCyc Sequence Dump]  
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NC_012967: 3878631..3877768<br />{{GBrowseFigureByCoord|3877768|3878631|REL606|NC_012967}}
NC_012967: 3878631..3877768<br /><gbrowseImage>
name=NC_012967:3877768..3878631
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|3877768|3878631|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3877768|3878631|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3877768|3878631|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|3877768|3878631|FASTA Dump}}  
|-
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[[BW2952]]
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NC_012759: 3803758..3804621<br /><gbrowseImage>
name=NC_012759:3803758..3804621
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|3803758|3804621|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|3803758|3804621|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 3718416..3719279<br />{{GBrowseFigureByCoord|3718416|3719279|ecoli_W3110|W3110}}
W3110: 3718416..3719279<br /><gbrowseImage>
name=NC_007779:3718416..3719279
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|3717416|3720279|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3717416|3720279|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3718416|3719279|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3718416|3719279|FASTA Dump}}  
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DH10B: 4013872..4013009<br />{{GBrowseFigureByCoord|4013009|4013872|ecoli_DH10B|DH10B}}
DH10B: 4013872..4013009<br /><gbrowseImage>
name=NC_010473:4013009..4013872
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|4011283|4015598|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4011283|4015598|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4011283|4015598|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4011283|4015598|FASTA Dump}}  


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{|   id="I46a9fd88526c3"  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="I46a9fd88526c3"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
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Coding Start (SO:0000323)
|
[[MG1655]]
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3915428
|
Edman degradation
|
PMID:7508444<br />
|


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18027.I46a9fd88526c3&page=18027&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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{| {{Prettytable}} id="H46a9fd889d2a5"  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="H46a9fd889d2a5"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{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}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04b802ce0dd"  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.18027.J4e04b802ce0dd&page=18027&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="C46a9fd8961142"  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="C46a9fd8961142"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAACCGCGGCGGCCCCCGAGAC  
Primer 2:CCAACCGCGGCGGCCCCCGAGAC  
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[[:Category:Kohara_Phage:2A1|2A1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=560 Genobase]
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PMID:3038334
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{|   id="N46a9fd8a0c52e"  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="N46a9fd8a0c52e"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG10104 EcoCyc:EG10104]
EcoCyc:EG10104
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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=EB0102 EchoBASE:EB0102]
EcoGene:EG10104
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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=b3733 EcoliGenExpDB:b3733]
RegulonDB:ECK120000100
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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=C4659 ECOL199310CYC:C4659]
[http://www.ncbi.nlm.nih.gov/gene?term=948243 GeneID:948243]
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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=EG10104 EcoGene:EG10104]
EchoBASE:EB0102
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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]]
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[http://BioCyc.org/ECOO157/new-image?object=ATPG ECOO157CYC:ATPG]
ASAP:ABE-0012211
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''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/27 CGSC:27]
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|-
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012211&formSubmitReturn=1 ASAP:ABE-0012211]
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Latest revision as of 20:49, 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

atpG

Mnemonic

ATP

Synonyms

ECK3726, b3733, JW3711, papC, uncG, unc[1]

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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

84.39 minutes, 84.39 minutes 

MG1655: 3916288..3915425
<gbrowseImage> name=NC_000913:3915425..3916288 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3878631..3877768
<gbrowseImage> name=NC_012967:3877768..3878631 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3803758..3804621
<gbrowseImage> name=NC_012759:3803758..3804621 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3718416..3719279
<gbrowseImage> name=NC_007779:3718416..3719279 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4013872..4013009
<gbrowseImage> name=NC_010473:4013009..4013872 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

3915428

Edman degradation

PMID:7508444[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

ΔatpG (Keio:JW3711)

deletion

deletion

PMID:16738554[3]

Shigen

atpG428

CGSC:7266


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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

JW3711

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCCGGCGCAAAAGAGATACG

Primer 2:CCAACCGCGGCGGCCCCCGAGAC

2A1

Kohara Phage

Genobase

PMID:3038334[5]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[6]

est. P1 cotransduction: 17% [7]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[6]

est. P1 cotransduction: 60% [7]
Synonyms:zie-296::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:EG10104

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10104

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000100

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948243

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0102

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012211

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. ↑ Tang, C et al. (1994) Structure of the gamma subunit of Escherichia coli F1 ATPase probed in trypsin digestion and biotin-avidin binding studies. J. Biol. Chem. 269 4467-72 PubMed
  3. ↑ 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. ↑ 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 CGSC: The Coli Genetics Stock Center
  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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