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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0107, b0108, JW0104''<ref name='LIB:Riley_2006'/>
''ECK0107, b0108, JW0104''<ref name='LIB:Riley_2006'/>, JW0104''


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{|   id="K46a9a89c4d029"  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="K46a9a89c4d029"  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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W3110: 117549..117109<br /><gbrowseImage>
W3110: 117549..117109<br /><gbrowseImage>
name=AC_000091:117109..117549
name=NC_007779:117109..117549
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|116109|118549|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|116109|118549|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|117109|117549|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|117109|117549|FASTA Dump}}  
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{|   id="G46a9a89ce99d6"  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="G46a9a89ce99d6"  class=" tableEdit Gene_sequence_features_table"   
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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="D46a9a89d35d4d"  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="D46a9a89d35d4d"  class=" tableEdit Gene_allele_table dataTable"   
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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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&Delta;ppdD (Keio:JW0104)
''ppdD(del)'' (Keio:JW0104)
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deletion
deletion
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PMID:16738554
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=106667 CGSC8386]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106667 CGSC8386]<ref name='LIB:cgsc'/>  
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&Delta;ppdD::kan
''ppdD(del)''::kan
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deletion
deletion
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&Delta;ppdD::kan
''ppdD(del)''::kan
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deletion
deletion
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''&#916;ppdD-726::kan''
''ppdD-726(del)::kan''
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{|   id="M4e04c1591f8df"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04c1591f8df"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="T46a9a89dd2003"  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="T46a9a89dd2003"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="V46a9a89e66ee5"  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="V46a9a89e66ee5"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:EG12107
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG12107
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[RegulonDB]]
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RegulonDB:ECK120002012
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=945817 GeneID:945817]
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Escherichia coli str. K-12 substr. MG1655
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[[EchoBASE]]
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EchoBASE:EB2031
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0000372
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:37, 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

ppdD

Mnemonic

Prepilin peptidase-dependent

Synonyms

ECK0107, b0108, JW0104[1], JW0104

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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

2.52 minutes 

MG1655: 117549..117109
<gbrowseImage> name=NC_000913:117109..117549 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 120353..119913
<gbrowseImage> name=NC_012967:119913..120353 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 117108..117548
<gbrowseImage> name=NC_012759:117108..117548 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 117549..117109
<gbrowseImage> name=NC_007779:117109..117549 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 91653..91213
<gbrowseImage> name=NC_010473:91213..91653 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

ppdD(del) (Keio:JW0104)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8386[3]

ppdD(del)::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938[4]

ppdD(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ppdD-726(del)::kan

PMID:16738554[2]

CGSC:102422


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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

JW0104

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGACAAGCAACGCGGTTTTAC

Primer 2:CCGTTGGCGTCATCAAAGCGGAA

15B8

Kohara Phage

Genobase

PMID:3038334[6]

4D12

Kohara Phage

Genobase

PMID:3038334[6]

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[3]

est. P1 cotransduction: 26% [7]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 29% [7]

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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:EG12107

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12107

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002012

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945817

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2031

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000372

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. ↑ 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. ↑ 4.0 4.1 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
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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