ppc:Gene: Difference between revisions

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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''ppc''  
''ppc''  
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3947, b3956, JW3928, asp, glu, pepC''<ref name='LIB:Riley_2006'/>
''ECK3947, b3956, JW3928, asp, glu, pepC''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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{{GBrowseFastaLink|ecoli|NC_000913|4148470|4151121|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|4148470|4151121|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10756 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10756 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3483583|3486234|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3483583|3486234|FASTA Dump}}  
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===Notes===
===Notes===
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====Notes====
====Notes====
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109118 CGSC10837]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109118 CGSC10837]<ref name='LIB:cgsc'/>  
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|[[PMID:13791860]]<ref name=PMID:13791860/>[[PMID:4874804]]<ref name=PMID:4874804/>[[PMID:14292146]]<ref name=PMID:14292146/>
[[PMID:13791860]]<ref name=PMID:13791860/> [[PMID:4874804]]<ref name=PMID:4874804/> [[PMID:14292146]]<ref name=PMID:14292146/>
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[[cgscmutation:7662|CGSC:7662]]
[[cgscmutation:7662|CGSC:7662]]
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|[[PMID:4874804]]<ref name=PMID:4874804/>[[PMID:14292146]]<ref name=PMID:14292146/>
[[PMID:4874804]]<ref name=PMID:4874804/> [[PMID:14292146]]<ref name=PMID:14292146/>
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[[cgscmutation:7826|CGSC:7826]]
[[cgscmutation:7826|CGSC:7826]]
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[[cgscmutation:102416|CGSC:102416]]
[[cgscmutation:102416|CGSC:102416]]
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===Notes===
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JW3928
JW3928
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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]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
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Primer 2:CCGCCGGTATTACGCATACCTGC  
Primer 2:CCGCCGGTATTACGCATACCTGC  
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[[pflD:Gene|pflD501::Tn10]]
[[pflD:Gene|pflD501::Tn10]]
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CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 84% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 84% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).  
 
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Synonyms:zij-501::Tn10  
 
 
CAG18477 also carries metF79(Am) (CGSC).  
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[[argE:Gene|argE86::Tn10]]
[[argE:Gene|argE86::Tn10]]
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est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/>  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[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=0012950&formSubmitReturn=1 ASAP:ABE-0012950]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012950&formSubmitReturn=1 ASAP:ABE-0012950]
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:37, 21 January 2009

{{#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 Alleles and Phenotypes 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

ppc

Mnemonic
Synonyms

ECK3947, b3956, JW3928, asp, glu, pepC[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

89.41 minutes, 89.41 minutes 

MG1655: 4151121..4148470
gbrowse_img.php?coord=4147470..4152121&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3483583..3486234
gbrowse_img.php?coord=3482583..3487234&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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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 Location Description
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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

Δppc (Keio:JW3928)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10837[3]

ppc-2

PMID:13791860[4]PMID:4874804[5]PMID:14292146[6]

CGSC:7662

ppc-1

PMID:4874804[5]PMID:14292146[6]

CGSC:7826

ppc-3

CGSC:10656

ppc-5::kan

CGSC:76204

Δppc-742::kan

PMID:16738554[2]

CGSC:102416


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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

JW3928

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAACGAACAATATTCCGCATT

Primer 2:CCGCCGGTATTACGCATACCTGC

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[3]

est. P1 cotransduction: 84% [8]nnSynonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

argE86::Tn10

Linked marker

CAG12185 = CGSC7471[3]

est. P1 cotransduction: 88% [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 (EcoliWiki Page)

EcoCyc:EG10756

EchoBASE (EcoliWiki Page)

EchoBASE:EB0749

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3956

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4915

EcoGene (EcoliWiki Page)

EcoGene:EG10756

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PPC

CGSC (EcoliWiki Page)

CGSC:368

ASAP (EcoliWikiPage)

ASAP:ABE-0012950


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Notes

Links

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Name URL Comments
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References

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  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. ↑ ADELBERG, EA & BURNS, SN (1960) Genetic variation in the sex factor of Escherichia coli. J. Bacteriol. 79 321-30 PubMed
  5. ↑ 5.0 5.1 Vanderwinkel, E & De Vlieghere, M (1968) [Physiology and genetics of isocitritase and the malate synthases of Escherichia coli]. Eur. J. Biochem. 5 81-90 PubMed
  6. ↑ 6.0 6.1 GLANSDORFF, N (1965) TOPOGRAPHY OF COTRANSDUCIBLE ARGININE MUTATIONS IN ESCHERICHIA COLI K-12. Genetics 51 167-79 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 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).


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