murE: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="Q46a9a8204f0f9"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''murE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''murE''
Murein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0086, b0085, JW0083''<ref name='LIB:Riley_2006'/>, JW0083''


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!{{table_heading_style}} |Synonyms
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''ECK0086, b0085, JW0083''<ref name='LIB:Riley_2006'/>
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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="L46a9a820c781e"  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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2.01 minutes&nbsp;
2.01 minutes&nbsp;
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MG1655: 93166..94653<br />{{GBrowseFigureByCoord|92166|95653|ecoli|MG1655}}
MG1655: 93166..94653<br /><gbrowseImage>
name=NC_000913:93166..94653
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10621 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10621 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:92166..95653 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|92166|95653|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:93166..94653&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|93166|94653|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10621 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10621 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
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NC_012967: 95970..97457<br /><gbrowseImage>
name=NC_012967:95970..97457
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|95970|97457|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|95970|97457|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 93165..94652<br /><gbrowseImage>
name=NC_012759:93165..94652
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|93165|94652|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|93165|94652|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 93166..94653<br />{{GBrowseFigureByCoord|92166|95653|ecoli_W3110|W3110}}  
W3110: 93166..94653<br /><gbrowseImage>
name=NC_007779:93166..94653
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|92166|95653|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:92166..95653 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|93166|94653|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:93166..94653&plugin_action=Go FASTA Dump]
[[DH10B]]
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DH10B: 67270..68757<br /><gbrowseImage>
name=NC_010473:67270..68757
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|64296|71731|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|64296|71731|FASTA Dump}}
 
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===Notes===
===Notes===
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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]]
|
93169
|
Edman degradation
|
PMID:2198024<br />PMID:2269304<br />
|
 
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====Notes====
====Notes====
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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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murEA495S
|
 
|
A495S
|
 
|
(in murE1)
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|
 
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Strain variation; seeded from [http://www.uniprot.org/uniprot/P22188 UniProt:P22188]
|-
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murEE344K
|
 
|
E344K
|
 
|
(in murE1)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P22188 UniProt:P22188]
|-
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''murE1''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9851|CGSC:9851]]
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|-
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''ispA P<sub>xyl</sub>-murE-B''
|
 
|
 
|
Growth Phenotype
|
repression of the murE-B operon allowed vigorous L-form growth.
|
PMID:23452849
|
Mutant Strain: LR2
|
Repression in Figure 2A 
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


Sequence of the ''murE1'' allele <ref name='PMID:9166795'/>. A strain with the ''murE1'' is temperature sensitive for growth. Mutants grow at 30C, but lyse at 42C. <ref name='PMID:4552998'/>
==Genetic Interactions==
{{BacktoTop}}
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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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JW0083
JW0083
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTGCAATCACCCCCAGCAGACG  
Primer 2:CCTGCAATCACCCCCAGCAGACG  
|-
|-
|
[[:Category:Kohara_Phage:6C1|6C1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=109 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6F3|6F3]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=110 Genobase]
|
PMID:3038334
|-  
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leuO3051::Tn10
leuO3051::Tn10
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CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  
Synonyms:zab-3051::Tn10  
|-  
 
 
The start of leuO was reannotated by Riley et al. (2006).  
|-
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|
[[yadC:Gene|zad-220::Tn10]]
[[yadC:Gene|zad-220::Tn10]]
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|
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est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10621 EcoCyc:EG10621] 
|
|
[[EcoCyc]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
EcoCyc:EG10621
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0616 EchoBASE:EB0616]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[EcoGene]]
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
EcoGene:EG10621
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0085 EcoliGenExpDB:b0085]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0103 ECOL199310CYC:C0103]
[http://www.ncbi.nlm.nih.gov/gene?term=944791 GeneID:944791]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10621 EcoGene:EG10621] 
RegulonDB:ECK120000614
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=MURE ECOO157CYC:MURE] 
EchoBASE:EB0616
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/475 CGSC:475] 
ASAP:ABE-0000311
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:mur genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 23:19, 12 August 2019

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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

murE

Mnemonic

Murein

Synonyms

ECK0086, b0085, JW0083[1], JW0083

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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

2.01 minutes 

MG1655: 93166..94653
<gbrowseImage> name=NC_000913:93166..94653 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 95970..97457
<gbrowseImage> name=NC_012967:95970..97457 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 93165..94652
<gbrowseImage> name=NC_012759:93165..94652 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 93166..94653
<gbrowseImage> name=NC_007779:93166..94653 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 67270..68757
<gbrowseImage> name=NC_010473:67270..68757 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

93169

Edman degradation

PMID:2198024[2]
PMID:2269304[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

murEA495S

A495S

(in murE1)

Strain variation; seeded from UniProt:P22188

murEE344K

E344K

(in murE1)

Strain variation; seeded from UniProt:P22188

murE1

CGSC:9851

ispA Pxyl-murE-B

Growth Phenotype

repression of the murE-B operon allowed vigorous L-form growth.

PMID:23452849[4]

Mutant Strain: LR2

Repression in Figure 2A

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Notes

Sequence of the murE1 allele [5]. A strain with the murE1 is temperature sensitive for growth. Mutants grow at 30C, but lyse at 42C. [6]

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

JW0083

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGCAGATCGTAATTTGCGCGA

Primer 2:CCTGCAATCACCCCCAGCAGACG

6C1

Kohara Phage

Genobase

PMID:3038334[8]

6F3

Kohara Phage

Genobase

PMID:3038334[8]

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[9]

est. P1 cotransduction: 72% [10]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[9]

est. P1 cotransduction: 7% [10]

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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:EG10621

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10621

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944791

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000614

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0616

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000311

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. ↑ Michaud, C et al. (1990) Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetylmuramyl-tripeptide synthetase of Escherichia coli. Biochem. J. 269 277-8 PubMed
  3. ↑ Michaud, C et al. (1990) Over-production, purification and properties of the uridine-diphosphate-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase from Escherichia coli. Eur. J. Biochem. 194 853-61 PubMed
  4. ↑ Mercier, R et al. (2013) Excess membrane synthesis drives a primitive mode of cell proliferation. Cell 152 997-1007 PubMed
  5. ↑ Eveland, SS et al. (1997) Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-gamma-glutamate ligases: identification of a ligase superfamily. Biochemistry 36 6223-9 PubMed
  6. ↑ Lugtenberg, EJ & v Schijndel-van Dam, A (1972) Temperature-sensitive mutants of Escherichia coli K-12 with low activities of the L-alanine adding enzyme and the D-alanyl-D-alanine adding enzyme. J. Bacteriol. 110 35-40 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 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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