ybbM:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ybbM}}{{Tab On|Gene|ybbM}}{{Tab|Gene Product(s)|ybbM}}{{Tab|Expression|ybbM}}{{Tab|Evolution|ybbM}}{{Tab|On One Page|ybbM}}{{TabsBottom}}
{{Tab|Quickview|ybbM}}{{Tab On|Gene|ybbM}}{{Tab|Gene Product(s)|ybbM}}{{Tab|Expression|ybbM}}{{Tab|Evolution|ybbM}}{{Tab|On One Page|ybbM}}{{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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ybbM''  
''ybbM''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0485, b0491, JW5066''<ref name='LIB:Riley_2006'/>, JW5066''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11547.N46a9b1f2d87b2&page=11547&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0485, b0491, JW5066''<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="H46a9b1f35c224"  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
|-
|-  
|
|
MG1655
MG1655
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11.12 minutes&nbsp;
11.12 minutes&nbsp;
|
|
MG1655: 515807..516586<br />{{GBrowseFigureByCoord|514807|517586|ecoli|MG1655}}
MG1655: 515807..516586<br /><gbrowseImage>
name=NC_000913:515807..516586
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6267 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6267 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:514807..517586 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|514807|517586|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:515807..516586&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|515807|516586|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6267 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6267 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 488751..489530<br /><gbrowseImage>
name=NC_012967:488751..489530
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|488751|489530|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|488751|489530|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 418566..419345<br /><gbrowseImage>
name=NC_012759:418566..419345
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|418566|419345|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|418566|419345|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 515807..516586<br />{{GBrowseFigureByCoord|514807|517586|ecoli_W3110|W3110}}  
W3110: 515807..516586<br /><gbrowseImage>
name=NC_007779:515807..516586
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|514807|517586|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|515807|516586|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:514807..517586 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:515807..516586&plugin_action=Go FASTA Dump]
DH10B: 455138..455917<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:455138..455917
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|453580|457475|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|453580|457475|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9b1f404513"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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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="E46a9b1f444594"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;ybbM (Keio:JW5066)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109437 CGSC11156]<ref name='LIB:cgsc'/>
|
|-
|
&Delta;ybbM::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|N-Acetyl-D-glucosamine]]
|
PMID:16095938
|
 
|
|-
|
&Delta;ybbM::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-D-Glucose-6-phosphate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;ybbM::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
''&#916;ybbM774::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:103664|CGSC:103664]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B4e04c6514e23b"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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|
 
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:7C12|7C12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=154 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8E4|8E4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=155 Genobase]
|
PMID:3038334
|-
|
[[gsk:Gene|gsk-3055::Tn10]]
|
Linked marker
|
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
|-
|
[[purK:Gene|purK79::Tn10]]
|
Linked marker
|
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:purE79::Tn10
 
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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
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G6267
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6267 EcoCyc:G6267] 
EcoGene:EG13260
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3048 EchoBASE:EB3048] 
RegulonDB:ECK120002875
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0491 EcoliGenExpDB:b0491]
[http://www.ncbi.nlm.nih.gov/gene?term=945137 GeneID:945137]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13260 EcoGene:EG13260] 
EchoBASE:EB3048
|
|
''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=YBBM ECOO157CYC:YBBM] 
ASAP:ABE-0001705
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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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:ybb genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

ybbM

Mnemonic

Systematic nomenclature

Synonyms

ECK0485, b0491, JW5066[1], JW5066

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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

11.12 minutes 

MG1655: 515807..516586
<gbrowseImage> name=NC_000913:515807..516586 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 488751..489530
<gbrowseImage> name=NC_012967:488751..489530 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 418566..419345
<gbrowseImage> name=NC_012759:418566..419345 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 515807..516586
<gbrowseImage> name=NC_007779:515807..516586 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 455138..455917
<gbrowseImage> name=NC_010473:455138..455917 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

ΔybbM (Keio:JW5066)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11156[3]

ΔybbM::kan

deletion

Biolog:respiration

unable to respire N-Acetyl-D-glucosamine

PMID:16095938[4]

ΔybbM::kan

deletion

Biolog:respiration

unable to respire a-D-Glucose-6-phosphate

PMID:16095938[4]

ΔybbM::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔybbM774::kan

PMID:16738554[2]

CGSC:103664


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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

7C12

Kohara Phage

Genobase

PMID:3038334[6]

8E4

Kohara Phage

Genobase

PMID:3038334[6]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 60% [7]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 23% [7]
Synonyms:purE79::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:G6267

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13260

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002875

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945137

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3048

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001705

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 4.2 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 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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