ppdC: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="H46a9e720b9393"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ppdC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ppdC''
Prepilin peptidase-dependent
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2819, b2823, JW2791, ygdA''<ref name='LIB:Riley_2006'/>, ygdA''


|-
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!{{table_heading_style}} |Synonyms
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''ECK2819, b2823, JW2791, ygdA''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='141836'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e72143a66"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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63.81 minutes&nbsp;
63.81 minutes&nbsp;
|
|
MG1655: 2960786..2960463<br />{{GBrowseFigureByCoord|2959463|2961786|ecoli|MG1655}}
MG1655: 2960786..2960463<br /><gbrowseImage>
name=NC_000913:2960463..2960786
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11154 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11154 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2959463..2961786 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2959463|2961786|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2960463..2960786&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2960463|2960786|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11154 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11154 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2857383..2857060<br /><gbrowseImage>
name=NC_012967:2857060..2857383
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2857060|2857383|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2857060|2857383|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2847611..2847934<br /><gbrowseImage>
name=NC_012759:2847611..2847934
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2847611|2847934|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2847611|2847934|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2961420..2961097<br />{{GBrowseFigureByCoord|2960097|2962420|ecoli_W3110|W3110}}  
W3110: 2961420..2961097<br /><gbrowseImage>
name=NC_007779:2961097..2961420
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2960097|2962420|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2961097|2961420|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 3054656..3054333<br /><gbrowseImage>
name=NC_010473:3054333..3054656
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2960097..2962420 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3053687|3055302|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2961097..2961420&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3053687|3055302|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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====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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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108464 CGSC10183]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108464 CGSC10183]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009257 ppdC::Tn5KAN-I-SceI] (FB20947)
|
Insertion at nt 267 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20947]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009257 ppdC::Tn5KAN-I-SceI] (FB20948)
|
Insertion at nt 267 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20948]
|
contains [[pKD46]]
|-  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:102420|CGSC:102420]]
[[cgscmutation:102420|CGSC:102420]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16213.F46a9e7224611f&page=16213&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==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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JW2791
JW2791
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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


Status:Clone OK
Status:Clone OK
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Primer 2:CCtTGACGATTCGGGCAATGCAG  
Primer 2:CCtTGACGATTCGGGCAATGCAG  
|-
|-
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[[:Category:Kohara_Phage:3G11|3G11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=460 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5A10|5A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=461 Genobase]
|
PMID:3038334
|-  
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[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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[[speA:Gene|speA210::Tn10]]
[[speA:Gene|speA210::Tn10]]
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CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10


Synonyms:zgd-210::Tn10, zgf-210::Tn10
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===Notes===
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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=EG11154 EcoCyc:EG11154] 
EcoCyc:EG11154
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1143 EchoBASE:EB1143] 
EcoGene:EG11154
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2823 EcoliGenExpDB:b2823] 
RegulonDB:ECK120001137
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://BioCyc.org/ECOL199310/new-image?object=C3417 ECOL199310CYC:C3417]
[http://www.ncbi.nlm.nih.gov/gene?term=945797 GeneID:945797]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11154 EcoGene:EG11154] 
EchoBASE:EB1143
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PPDC ECOO157CYC:PPDC] 
ASAP:ABE-0009257
|
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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 in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ppd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

ppdC

Mnemonic

Prepilin peptidase-dependent

Synonyms

ECK2819, b2823, JW2791, ygdA[1], ygdA

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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

63.81 minutes 

MG1655: 2960786..2960463
<gbrowseImage> name=NC_000913:2960463..2960786 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2857383..2857060
<gbrowseImage> name=NC_012967:2857060..2857383 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2847611..2847934
<gbrowseImage> name=NC_012759:2847611..2847934 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2961420..2961097
<gbrowseImage> name=NC_007779:2961097..2961420 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3054656..3054333
<gbrowseImage> name=NC_010473:3054333..3054656 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

ΔppdC (Keio:JW2791)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10183[3]

ppdC::Tn5KAN-I-SceI (FB20947)

Insertion at nt 267 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20947

does not contain pKD46

ppdC::Tn5KAN-I-SceI (FB20948)

Insertion at nt 267 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20948

contains pKD46

ΔppdC748::kan

PMID:16738554[2]

CGSC:102420


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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

JW2791

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAGCTTCCCTGAAGAATCA

Primer 2:CCtTGACGATTCGGGCAATGCAG

3G11

Kohara Phage

Genobase

PMID:3038334[6]

5A10

Kohara Phage

Genobase

PMID:3038334[6]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 72% [7]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: % [7]
Synonyms:zgd-210::Tn10, zgf-210::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:EG11154

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11154

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001137

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945797

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1143

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009257

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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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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