adhE:Gene: Difference between revisions

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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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''ECK1235, b1241, JW1228, adhC, ana''<ref name='LIB:Riley_2006'/>
''ECK1235, b1241, JW1228, adhC, ana''<ref name='LIB:Riley_2006'/>, ana''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9c2c56d85d"  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: 1297344..1294669<br /><gbrowseImage>
MG1655: 1297344..1294669<br /><gbrowseImage>
name=NC_000913:1294669..1297344
name=NC_000913:1294669..1297344
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10031 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10031 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1293669|1298344|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1293669|1298344|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1294669|1297344|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1294669|1297344|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10031 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10031 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|1184167|NC_1186842|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1184167|1186842|GBrowse (BW2952)}}
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W3110: 1299698..1297023<br /><gbrowseImage>
W3110: 1299698..1297023<br /><gbrowseImage>
name=AC_000091:1297023..1299698
name=NC_007779:1297023..1299698
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|1296023|1300698|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1296023|1300698|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|NC_007779|1297023|1299698|FASTA Dump}}  
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DH10B: 1337585..1334910<br /><gbrowseImage>
DH10B: 1337585..1334910<br /><gbrowseImage>
name=NC_010473:1334910..1337585
name=NC_010473:1334910..1337585
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|ecoli_DH10B|NC_010473|1329560|1342935|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1329560|1342935|GBrowse(DH10B)}}
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{|   id="M46a9c2c61aa25"  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="M46a9c2c61aa25"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="H46a9c2c65c1a8"  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="H46a9c2c65c1a8"  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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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004164 adhE]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004164 adhE::Tn5KAN-2] (FB20272)
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Insertion at nt 1923 in Plus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20272]
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At position 1923 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20272
does not contain [[pKD46]]  
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13047.W4e04b6f09ef7c-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W4e04b6f09ef7c"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="N46a9c2c70901f"  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="N46a9c2c70901f"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAGCGGATTTTTTCGCTTTTTT  
Primer 2:CCAGCGGATTTTTTCGCTTTTTT  
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[[:Category:Kohara_Phage:4D8|4D8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=250 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:3D5|3D5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=251 Genobase]
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PMID:3038334
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{|   id="G46a9c2c79567c"  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="G46a9c2c79567c"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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!|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=EG10031 EcoCyc:EG10031]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0030 EchoBASE:EB0030]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1241 EcoliGenExpDB:b1241]
EcoCyc:EG10031
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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]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C1705 ECOL199310CYC:C1705]
EcoGene:EG10031
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10031 EcoGene:EG10031]
RegulonDB:ECK120000028
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=ADHE ECOO157CYC:ADHE]
[http://www.ncbi.nlm.nih.gov/gene?term=945837 GeneID:945837]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1041 CGSC:1041]
EchoBASE:EB0030
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004164&formSubmitReturn=1 ASAP:ABE-0004164]
ASAP:ABE-0004164
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:30, 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

adhE

Mnemonic

Alcohol/acetaldehyde dehydrogenase

Synonyms

ECK1235, b1241, JW1228, adhC, ana[1], ana

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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

27.9 minutes 

MG1655: 1297344..1294669
<gbrowseImage> name=NC_000913:1294669..1297344 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1296914..1294239
<gbrowseImage> name=NC_012967:1294239..1296914 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1184167..1186842
<gbrowseImage> name=NC_012759:1184167..1186842 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1299698..1297023
<gbrowseImage> name=NC_007779:1297023..1299698 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1337585..1334910
<gbrowseImage> name=NC_010473:1334910..1337585 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

1294672

Edman degradation

PMID:2015910[2]
PMID:2695398[3]


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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

ΔadhE (Keio:JW1228)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC9113[5]

adhE::Tn5KAN-2 (FB20272)

Insertion at nt 1923 in Plus orientation

PMID:15262929[6]

E. coli Genome Project:FB20272

does not contain pKD46

ΔadhE::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938[7]

ana-1

CGSC:5096

adhE80

PMID:6986356[8]

CGSC:7028

adhE1

PMID:6752127[9]

CGSC:7285

adhE16(ts)

temperature sensitive

CGSC:7289

adhE2

PMID:6752127[9]

CGSC:7457

ana-2

adhE

CGSC:14693

adhE36

PMID:3550385[10]

CGSC:92529

adhE38

PMID:3550385[10]

CGSC:92530

ΔadhE748::kan

PMID:16738554[4]

CGSC:99914


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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

JW1228

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCGCTGTTACTAATGTCGCTGA

Primer 2:CCAGCGGATTTTTTCGCTTTTTT

4D8

Kohara Phage

Genobase

PMID:3038334[12]

3D5

Kohara Phage

Genobase

PMID:3038334[12]

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[5]

est. P1 cotransduction: 4% [13]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[5]

est. P1 cotransduction: 73% [13]
Synonyms:zch-506::Tn10, zci-506::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:EG10031

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10031

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000028

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945837

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0030

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004164

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. ↑ Kessler, D et al. (1991) Pyruvate-formate-lyase-deactivase and acetyl-CoA reductase activities of Escherichia coli reside on a polymeric protein particle encoded by adhE. FEBS Lett. 281 59-63 PubMed
  3. ↑ Goodlove, PE et al. (1989) Cloning and sequence analysis of the fermentative alcohol-dehydrogenase-encoding gene of Escherichia coli. Gene 85 209-14 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ 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
  8. ↑ Clark, D & Cronan, JE Jr (1980) Escherichia coli mutants with altered control of alcohol dehydrogenase and nitrate reductase. J. Bacteriol. 141 177-83 PubMed
  9. ↑ 9.0 9.1 Lorowitz, W & Clark, D (1982) Escherichia coli mutants with a temperature-sensitive alcohol dehydrogenase. J. Bacteriol. 152 935-8 PubMed
  10. ↑ 10.0 10.1 Cunningham, PR & Clark, DP (1986) The use of suicide substrates to select mutants of Escherichia coli lacking enzymes of alcohol fermentation. Mol. Gen. Genet. 205 487-93 PubMed
  11. ↑ 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
  12. ↑ 12.0 12.1 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
  13. ↑ 13.0 13.1 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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