ppiD: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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{|   id="H46a9b090a81b9" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''ppiD''  
''ppiD''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Peptidylprolyl isomerase
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0435, b0441, JW0431, ybaU''<ref name='LIB:Riley_2006'/>
''ECK0435, b0441, JW0431, ybaU''<ref name='LIB:Riley_2006'/>, ybaU''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b0915b9be"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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9.94 minutes&nbsp;
9.94 minutes&nbsp;
|
|
MG1655: 461139..463010<br />{{GBrowseFigureByCoord|461139|463010|ecoli|MG1655}}
MG1655: 461139..463010<br /><gbrowseImage>
name=NC_000913:461139..463010
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6242 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6242 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|460139|464010|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|460139|464010|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|461139|463010|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|461139|463010|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6242 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6242 EcoCyc Sequence Dump]  
|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 461139..463010<br />{{GBrowseFigureByCoord|461139|463010|ecoli_W3110|W3110}}
NC_012967: 433970..435841<br /><gbrowseImage>
name=NC_012967:433970..435841
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|460139|464010|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|433970|435841|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|461139|463010|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|433970|435841|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
 
|
|
NC_012759: 363898..365769<br /><gbrowseImage>
name=NC_012759:363898..365769
source=BW2952
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 400470..402341<br />{{GBrowseFigureByCoord|400470|402341|ecoli_DH10B|DH10B}}
{{GBrowseLink|BW2952|NC_012759|363898|365769|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|363898|365769|FASTA Dump}}
|-
|
W3110
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|396728|406083|GBrowse(DH10B)}}
&nbsp;
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|396728|406083|FASTA Dump}}  
W3110: 461139..463010<br /><gbrowseImage>
name=NC_007779:461139..463010
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|460139|464010|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|461139|463010|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 433970..435841<br />{{GBrowseFigureByCoord|433970|435841|REL606|NC_012967}}
DH10B: 400470..402341<br /><gbrowseImage>
name=NC_010473:400470..402341
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|433970|435841|GBrowse (REL606)}}
{{GBrowseLink|DH10B|NC_010473|396728|406083|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|433970|435841|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|396728|406083|FASTA Dump}}  


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9b092589fc"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46a9b092c72d6"  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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|
|
   
   
|-
|
ppiDG312A,R
|
|
G312A,R
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0ADY1 UniProt:P0ADY1]
|-
|
ppiDG313A,R
|
|
G313A,R
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0ADY1 UniProt:P0ADY1]
|-
|
ppiDG347A
|
|
G347A
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0ADY1 UniProt:P0ADY1]
|-
|
ppiDI350A,F
|
|
I350A,F
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0ADY1 UniProt:P0ADY1]
|-  
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|
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11447.M4e04c15ff24c9-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTGCTGTTCCAGCGCATCGCC  
Primer 2:CCTTGCTGTTCCAGCGCATCGCC  
|-
|
[[:Category:Kohara_Phage:3B6|3B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=148 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7E2|7E2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=149 Genobase]
|
PMID:3038334
|-  
|-  
|
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Synonyms:zbb-30-55::TnlO, zba-3055::Tn10  
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=G6242 EcoCyc:G6242]
EcoCyc:G6242
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3038 EchoBASE:EB3038]
EcoGene:EG13249
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0441 EcoliGenExpDB:b0441]
RegulonDB:ECK120002853
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0557 ECOL199310CYC:C0557]
[http://www.ncbi.nlm.nih.gov/gene?term=946056 GeneID:946056]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13249 EcoGene:EG13249]
EchoBASE:EB3038
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YBAU ECOO157CYC:YBAU]
ASAP:ABE-0001531
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001531&formSubmitReturn=1 ASAP:ABE-0001531]
|


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!|Name!!URL!!Comments


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ppi genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:ppi genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ppiD

Mnemonic

Peptidylprolyl isomerase

Synonyms

ECK0435, b0441, JW0431, ybaU[1], ybaU

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Notes

Location(s) and DNA Sequence

[back to top]


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

9.94 minutes 

MG1655: 461139..463010
<gbrowseImage> name=NC_000913:461139..463010 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 433970..435841
<gbrowseImage> name=NC_012967:433970..435841 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 363898..365769
<gbrowseImage> name=NC_012759:363898..365769 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 461139..463010
<gbrowseImage> name=NC_007779:461139..463010 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 400470..402341
<gbrowseImage> name=NC_010473:400470..402341 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

ΔppiD (Keio:JW0431)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8594[3]

ppiDG312A,R

G312A,R

Loss of activity

seeded from UniProt:P0ADY1

ppiDG313A,R

G313A,R

Loss of activity

seeded from UniProt:P0ADY1

ppiDG347A

G347A

Loss of activity

seeded from UniProt:P0ADY1

ppiDI350A,F

I350A,F

Loss of activity

seeded from UniProt:P0ADY1

zaj-3054::Tn10

Insertion at 461,486 bp in MG1655 (NC_000913)

adapted from Nichols et al.[4]

CAG12017 = CGSC7339[3]

Synonyms: zba-3054::Tn10

ΔppiD727::kan

PMID:16738554[2]

CGSC:102434


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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

JW0431

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCATGGACAGCTTACGCACGGC

Primer 2:CCTTGCTGTTCCAGCGCATCGCC

3B6

Kohara Phage

Genobase

PMID:3038334[6]

7E2

Kohara Phage

Genobase

PMID:3038334[6]

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[3]

est. P1 cotransduction: 32% [4]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 18% [4]
Synonyms:zbb-30-55::TnlO, zba-3055::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:G6242

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13249

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002853

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946056

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3038

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001531

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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 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).
  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

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