ppiD:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!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="W46a9b092c72d6"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6242 ECOCYC:G6242]
EcoCyc:G6242
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13249 EcoGene:EG13249]
EcoGene:EG13249
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120002853
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3038
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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-0001531
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:13, 27 May 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

ppiD

Mnemonic

Peptidylprolyl isomerase

Synonyms

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

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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

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=AC_000091:461139..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

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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

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

NCBI (EcoliWiki Page)

GeneID:946056

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002853

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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