rhmD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|yfaW}}{{Tab On|Gene|yfaW}}{{Tab|Gene Product(s)|yfaW}}{{Tab|Expression|yfaW}}{{Tab|Evolution|yfaW}}{{Tab|On One Page|yfaW}}{{TabsBottom}}
{{Tab|Quickview|rhmD}}{{Tab On|Gene|rhmD}}{{Tab|Gene Product(s)|rhmD}}{{Tab|Expression|rhmD}}{{Tab|Evolution|rhmD}}{{Tab|On One Page|rhmD}}{{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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yfaW''  
''rhmD''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2240, b2247, JW2241''<ref name='LIB:Riley_2006'/>
''ECK2240, b2247, JW2241'', yfaW<ref name='LIB:Riley_2006'/>, JW2241, yfaW''
|-
 
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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="H46a9d9855d4f8"  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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MG1655
MG1655
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50.83 minutes, 50.83 minutes&nbsp;
50.83 minutes, 50.83 minutes&nbsp;
|
|
MG1655: 2359448..2358231<br />{{GBrowseFigureByCoord|2357231|2360448|ecoli|MG1655}}
MG1655: 2359448..2358231<br /><gbrowseImage>
name=NC_000913:2358231..2359448
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7160 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7160 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2357231..2360448 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|2357231|2360448|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2358231..2359448&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|2358231|2359448|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7160 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7160 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2307939..2306722<br /><gbrowseImage>
name=NC_012967:2306722..2307939
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2306722|2307939|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2306722|2307939|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2244036..2245253<br /><gbrowseImage>
name=NC_012759:2244036..2245253
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|2244036|NC_2245253|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|2244036|NC_2245253|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 2366096..2364879<br />{{GBrowseFigureByCoord|2363879|2367096|ecoli_W3110|W3110}}  
W3110: 2366096..2364879<br /><gbrowseImage>
name=NC_007779:2364879..2366096
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|2363879|2367096|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2363879..2367096 GBrowse(W3110)]
{{GBrowseFastaLink|ecoli_W3110|NC_007779|2364879|2366096|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2364879..2366096&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 2450436..2449219<br /><gbrowseImage>
name=NC_010473:2449219..2450436
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|2446785|2452870|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2446785|2452870|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| {{Prettytable}} id="V46a9d986586d9"  class=" tableEdit Gene_allele_table dataTable" 
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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
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&Delta;yfaW (Keio:JW2241)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108088 CGSC9807]<ref name='LIB:cgsc'/>
|
|-
|
yfaWH29N
|
 
|
H29N
|
 
|
Loss of activity due to absence of substrate binding
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P77215 UniProt:P77215]
|-
|
yfaWH277N
|
 
|
H277N
|
 
|
35-fold decrease in activity. 59- fold decrease in substrate affinity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P77215 UniProt:P77215]
|-
|
yfaWH325N
|
 
|
H325N
|
 
|
Loss of activity. 2-fold decrease in substrate affinity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P77215 UniProt:P77215]
|-
|
''&#916;yfaW728::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:104632|CGSC:104632]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2241
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGAGAACATCATGACCCTACC
 
Primer 2:CCGTGGCTGTAGGGGCGTTTCAA
|-
|
[[:Category:Kohara_Phage:22C4|22C4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=378 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4B4|4B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=379 Genobase]
|
PMID:3038334
|-
|
[[yfaL:Gene|zfa-723::Tn10]]
|
Linked marker
|
CAG12178 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44155 CGSC7526]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 58% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).
|-
|
[[yfbO:Gene|zfb-223::Tn10]]
|
Linked marker
|
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zej-223::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7160 EcoCyc:G7160] 
EcoCyc:G7160
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3838 EchoBASE:EB3838] 
EchoBASE:EB3838
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2247 EcoliGenExpDB:b2247]
[http://chase.ou.edu/macro/searchlink.php?bnum=b2247 EcoliGenExpDB:b2247]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2789 ECOL199310CYC:C2789]
[http://BioCyc.org/ECOL199310/new-image?object=C2789 ECOL199310CYC:C2789]
|
|
   
   
|-
|-  
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|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14085 EcoGene:EG14085] 
EcoGene:EG14085
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z3505 ECOO157CYC:Z3505]
[http://BioCyc.org/ECOO157/new-image?object=Z3505 ECOO157CYC:Z3505]
|
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[[ASAP]]
|
ASAP:ABE-0007436
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7160 ECOCYC:G7160]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=945881 GeneID:945881]
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Escherichia coli str. K-12 substr. MG1655
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[[RegulonDB]]
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RegulonDB:ECK120003736
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 
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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:yfa genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

rhmD

Mnemonic
Synonyms

ECK2240, b2247, JW2241, yfaW[1], JW2241, yfaW

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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

50.83 minutes, 50.83 minutes 

MG1655: 2359448..2358231
<gbrowseImage> name=NC_000913:2358231..2359448 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2307939..2306722
<gbrowseImage> name=NC_012967:2306722..2307939 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2244036..2245253
<gbrowseImage> name=NC_012759:2244036..2245253 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2366096..2364879
<gbrowseImage> name=NC_007779:2364879..2366096 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2450436..2449219
<gbrowseImage> name=NC_010473:2449219..2450436 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

ΔyfaW (Keio:JW2241)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9807[3]

yfaWH29N

H29N

Loss of activity due to absence of substrate binding

seeded from UniProt:P77215

yfaWH277N

H277N

35-fold decrease in activity. 59- fold decrease in substrate affinity

seeded from UniProt:P77215

yfaWH325N

H325N

Loss of activity. 2-fold decrease in substrate affinity

seeded from UniProt:P77215

ΔyfaW728::kan

PMID:16738554[2]

CGSC:104632


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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

JW2241

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGAGAACATCATGACCCTACC

Primer 2:CCGTGGCTGTAGGGGCGTTTCAA

22C4

Kohara Phage

Genobase

PMID:3038334[5]

4B4

Kohara Phage

Genobase

PMID:3038334[5]

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[3]

est. P1 cotransduction: 58% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[3]

est. P1 cotransduction: 29% [6]
Synonyms:zej-223::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:G7160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3838

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2247

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2789

EcoGene

EcoGene:EG14085

Escherichia coli str. K-12 substr. MG1655

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z3505

ASAP

ASAP:ABE-0007436

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:G7160

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945881

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003736

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. ↑ 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. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 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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