fabF: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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{|{{Prettytable}}
{|  id="B46a9bf736ca0f"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''fabF''  
''fabF''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Fatty acid biosynthesis
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1081, b1095, JW1081, cvc, fabJ, vtr, vtrB''<ref name='LIB:Riley_2006'/>
''ECK1081, b1095, JW1081, cvc, fabJ, vtr, vtrB''<ref name='LIB:Riley_2006'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='131417'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9bf73e63f2"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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MG1655
MG1655
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24.81 minutes&nbsp;
24.81 minutes&nbsp;
|
|
MG1655: 1151162..1152403<br />{{GBrowseFigureByCoord|1150162|1153403|ecoli|MG1655}}
MG1655: 1151162..1152403<br /><gbrowseImage>
name=NC_000913:1151162..1152403
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12606 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12606 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1150162|1153403|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1150162|1153403|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1151162..1152403&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1151162|1152403|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12606 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12606 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 1166508..1167749<br /><gbrowseImage>
name=NC_012967:1166508..1167749
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1166508|1167749|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1166508|1167749|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1055087..1056328<br /><gbrowseImage>
name=NC_012759:1055087..1056328
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1055087|1056328|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|1055087|1056328|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1153516..1154757<br />{{GBrowseFigureByCoord|1152516|1155757|ecoli_W3110|W3110}}  
W3110: 1153516..1154757<br /><gbrowseImage>
name=NC_007779:1153516..1154757
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1152516|1155757|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1153516|1154757|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1206607..1207848<br /><gbrowseImage>
name=NC_010473:1206607..1207848
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1152516|1155757|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|1204125|1210330|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1153516..1154757&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1204125|1210330|FASTA Dump}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9bf7491cbc"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
1151165
|
Edman degradation
|
PMID:7972002<br />
|
 
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R46a9bf74d2ee3"  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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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107310 CGSC9029]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107310 CGSC9029]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0003705 fabF::Tn5KAN-2] (FB20101)
|
Insertion at nt 908 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20101]
|
does not contain [[pKD46]]
|-  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100774|CGSC:100774]]
[[cgscmutation:100774|CGSC:100774]]
|
|
   
   
|-
|
fabF
|
deletion
|


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Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


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


==Genetic Resources==
==Genetic Resources==
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JW1081
JW1081
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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:CCGATCTTTTTAAAGATCAAAGA  
Primer 2:CCGATCTTTTTAAAGATCAAAGA  
|-
|-
|
[[:Category:Kohara_Phage:14C1|14C1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=235 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:E9G1|E9G1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=236 Genobase]
|
PMID:3038334
|-  
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[[yccE:Gene|zcc-282::Tn10]]
[[yccE:Gene|zcc-282::Tn10]]
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[yceG:Gene|zce-726::Tn10]]
[[yceG:Gene|zce-726::Tn10]]
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|
|
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9bf7616097"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12606 EcoCyc:EG12606]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2490 EchoBASE:EB2490]
EcoCyc:EG12606
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1095 EcoliGenExpDB:b1095]
EcoGene:EG12606
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1365 ECOL199310CYC:C1365]
RegulonDB:ECK120002329
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG12606 EcoGene:EG12606]
|
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=FABF ECOO157CYC:FABF]
[http://www.ncbi.nlm.nih.gov/gene?term=946665 GeneID:946665]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/795 CGSC:795]
EchoBASE:EB2490
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003705&formSubmitReturn=1 ASAP:ABE-0003705] 
ASAP:ABE-0003705
|
|
''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:fab genes]]
[[Category:fab genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 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

fabF

Mnemonic

Fatty acid biosynthesis

Synonyms

ECK1081, b1095, JW1081, cvc, fabJ, vtr, vtrB[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

24.81 minutes 

MG1655: 1151162..1152403
<gbrowseImage> name=NC_000913:1151162..1152403 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1166508..1167749
<gbrowseImage> name=NC_012967:1166508..1167749 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1055087..1056328
<gbrowseImage> name=NC_012759:1055087..1056328 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1153516..1154757
<gbrowseImage> name=NC_007779:1153516..1154757 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1206607..1207848
<gbrowseImage> name=NC_010473:1206607..1207848 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

1151165

Edman degradation

PMID:7972002[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

ΔfabF (Keio:JW1081)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9029[4]

fabF::Tn5KAN-2 (FB20101)

Insertion at nt 908 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20101

does not contain pKD46

fabF200

CGSC:7259

fabF202

CGSC:8804

ΔfabF759::kan

PMID:16738554[3]

CGSC:100774

fabF

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[6]

fig 2

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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

JW1081

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCTCTAAGCGTCGTGTAGTTGT

Primer 2:CCGATCTTTTTAAAGATCAAAGA

14C1

Kohara Phage

Genobase

PMID:3038334[8]

E9G1

Kohara Phage

Genobase

PMID:3038334[8]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[4]

est. P1 cotransduction: % [9]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[4]

est. P1 cotransduction: 87% [9]

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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:EG12606

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12606

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002329

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946665

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2490

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003705

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. ↑ Siggaard-Andersen, M et al. (1994) The fabJ-encoded beta-ketoacyl-[acyl carrier protein] synthase IV from Escherichia coli is sensitive to cerulenin and specific for short-chain substrates. Proc. Natl. Acad. Sci. U.S.A. 91 11027-31 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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