argA:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
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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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2814, b2818, JW2786, Arg1, Arg2''<ref name='LIB:Riley_2006'/>
''ECK2814, b2818, JW2786, Arg1, Arg2''<ref name='LIB:Riley_2006'/>, Arg2, argB''


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{|   id="K46a9e6ff48a2a"  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="K46a9e6ff48a2a"  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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MG1655: 2947264..2948595<br /><gbrowseImage>
MG1655: 2947264..2948595<br /><gbrowseImage>
name=NC_000913:2947264..2948595
name=NC_000913:2947264..2948595
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10063 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10063 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2946264|2949595|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2946264|2949595|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2947264|2948595|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2947264|2948595|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10063 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10063 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2834412|NC_2835743|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2834412|2835743|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|2834412|NC_2835743|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|2834412|2835743|FASTA Dump}}  
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W3110: 2947898..2949229<br /><gbrowseImage>
W3110: 2947898..2949229<br /><gbrowseImage>
name=AC_000091:2947898..2949229
name=NC_007779:2947898..2949229
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|2946898|2950229|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2946898|2950229|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2947898|2949229|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2947898|2949229|FASTA Dump}}  
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DH10B: 3041134..3042465<br /><gbrowseImage>
DH10B: 3041134..3042465<br /><gbrowseImage>
name=NC_010473:3041134..3042465
name=NC_010473:3041134..3042465
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|3038472|3045127|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3038472|3045127|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3038472|3045127|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3038472|3045127|FASTA Dump}}  


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{|   id="X46a9e70004884"  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="X46a9e70004884"  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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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="I46a9e7004b9db"  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="I46a9e7004b9db"  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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''ΔargA743::kan''
''ΔargA743::kan''
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deletion
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deletion
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Auxotrophies
Auxotrophies
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16203.A4e04b77dd16f0-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04b77dd16f0"  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.16203.A4e04b77dd16f0&page=16203&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16203.A4e04b77dd16f0--></protect>
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="A46a9e70107243"  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="A46a9e70107243"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCgCCTAAATCCGCCATCAACAC  
Primer 2:CCgCCTAAATCCGCCATCAACAC  
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[[:Category:Kohara_Phage:10B6|10B6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=459 Genobase]
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PMID:3038334
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{|   id="M46a9e7019f8e9"  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="M46a9e7019f8e9"  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=EG10063 EcoCyc:EG10063]
EcoCyc:EG10063
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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=EB0061 EchoBASE:EB0061]
EcoGene:EG10063
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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=b2818 EcoliGenExpDB:b2818]
RegulonDB:ECK120000059
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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=C3412 ECOL199310CYC:C3412]
[http://www.ncbi.nlm.nih.gov/gene?term=947289 GeneID:947289]
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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=EG10063 EcoGene:EG10063]
EchoBASE:EB0061
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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=ARGA ECOO157CYC:ARGA]
ASAP:ABE-0009245
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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/1021 CGSC:1021]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009245&formSubmitReturn=1 ASAP:ABE-0009245]
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{|   id="M46a7034466271"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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Latest revision as of 20:44, 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

argA

Mnemonic

Arginine

Synonyms

ECK2814, b2818, JW2786, Arg1, Arg2[1], Arg2, argB

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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

63.52 minutes 

MG1655: 2947264..2948595
<gbrowseImage> name=NC_000913:2947264..2948595 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2843861..2845192
<gbrowseImage> name=NC_012967:2843861..2845192 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2834412..2835743
<gbrowseImage> name=NC_012759:2834412..2835743 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2947898..2949229
<gbrowseImage> name=NC_007779:2947898..2949229 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3041134..3042465
<gbrowseImage> name=NC_010473:3041134..3042465 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

2947267

Edman degradation

PMID:3320971[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

argAR58H

R58H

Auxotrophies

In EE11

seeded from UniProt:P0A6C5

argAH15Y

H15Y

Auxotrophies

In EE17

seeded from UniProt:P0A6C5

argAY19C

Y19C

Auxotrophies

In EE51

seeded from UniProt:P0A6C5

argAG287S

G287S

Auxotrophies

In PT2M216

seeded from UniProt:P0A6C5

argAQ432R

Q432R

Auxotrophies

In PT2M217

seeded from UniProt:P0A6C5

argAS54N

S54N

Auxotrophies

In PT2M217

seeded from UniProt:P0A6C5

ΔargA (Keio:JW2786)

deletion

deletion

Auxotrophies

PMID:16738554[3]

Shigen

CGSC10181[4]

argA::Tn5KAN-I-SceI (FB20943)

Insertion at nt 933 in Plus orientation

Auxotrophies

PMID:15262929[5]

E. coli Genome Project:FB20943

contains pKD46

argA::Tn5KAN-I-SceI (FB20944)

Insertion at nt 933 in Plus orientation

Auxotrophies

PMID:15262929[5]

E. coli Genome Project:FB20944

does not contain pKD46

argA21

Auxotrophies

CGSC:5137

argA42

Auxotrophies

CGSC:5157

argA52

Auxotrophies

CGSC:5167

argA76(Fs)

Auxotrophies

CGSC:5192

frameshift mutation

argA103

Auxotrophies

CGSC:5207

argA22

Auxotrophies

CGSC:6000

argA81::Tn10

Auxotrophies

CGSC:7098

argA9999

Auxotrophies

CGSC:9194

ΔargA743::kan

deletion

deletion

Auxotrophies

PMID:16738554[3]

CGSC:100036


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Notes

Genetic Interactions

[back to top]



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

JW2786

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGTAAAGGAACGTAAAACCGA

Primer 2:CCgCCTAAATCCGCCATCAACAC

10B6

Kohara Phage

Genobase

PMID:3038334[7]

fucP3072::Tn10

Linked marker

CAG12079 = CGSC7427[4]

est. P1 cotransduction: 59% [8]
Synonyms:fuc-3072::Tn10

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[4]

est. P1 cotransduction: 89% [8]

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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:EG10063

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10063

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000059

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947289

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0061

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009245

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. ↑ Brown, K et al. (1987) Complete nucleotide sequence of the Escherichia coli argA gene. Nucleic Acids Res. 15 10586 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 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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