ppiC:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

ppiC

Gene Synonym(s)

ECK3767, b3775, JW3748, parvA[1], parvA

Product Desc.

peptidyl-prolyl cis-trans isomerase C (rotamase C)[2][3]

Peptidylprolyl-cis-trans isomerase C, rotamase[4]

Product Synonyms(s)

peptidyl-prolyl cis-trans isomerase C (rotamase C)[1], B3775[2][1], PpiC[2][1], Par10[2][1] , ECK3767, JW3748, parvA, b3775

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ppiC[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

ppiC

Mnemonic

Peptidylprolyl isomerase

Synonyms

ECK3767, b3775, JW3748, parvA[1], parvA

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> 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

85.3 minutes, 85.3 minutes 

MG1655: 3957836..3957555
<gbrowseImage> name=NC_000913:3957555..3957836 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3921615..3921334
<gbrowseImage> name=NC_012967:3921334..3921615 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3847224..3847505
<gbrowseImage> name=NC_012759:3847224..3847505 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3676868..3677149
<gbrowseImage> name=NC_007779:3676868..3677149 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4056756..4056475
<gbrowseImage> name=NC_010473:4056475..4056756 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

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

Coding Start (SO:0000323)

MG1655

3957558

Edman degradation

PMID:8163020


edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔppiC (Keio:JW3748)

deletion

deletion

PMID:16738554

Shigen
CGSC10736[5]

ΔppiC726::kan

PMID:16738554

CGSC:102432


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3748

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAAAAACAGCAGCAGCACT

Primer 2:CCGTTGCGGTACAGCACCTTAAT

2A8

Kohara Phage

Genobase

PMID:3038334

2E6

Kohara Phage

Genobase

PMID:3038334

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[5]

est. P1 cotransduction: 86% [6]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 9% [6]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12352

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12352

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002222

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948285

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2256

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012334

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

PpiC

Synonyms

peptidyl-prolyl cis-trans isomerase C (rotamase C)[1], B3775[2][1], PpiC[2][1], Par10[2][1] , ECK3767, JW3748, parvA, b3775

Product description

peptidyl-prolyl cis-trans isomerase C (rotamase C)[2][3]

Peptidylprolyl-cis-trans isomerase C, rotamase[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0003755

peptidyl-prolyl cis-trans isomerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.2.1.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0003755

peptidyl-prolyl cis-trans isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0697

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006457

protein folding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0697

P

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000297

F

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

accA

PMID:15690043

Experiment(s):EBI-884491

Protein

accD

PMID:15690043

Experiment(s):EBI-884491

Protein

rplD

PMID:15690043

Experiment(s):EBI-884491

Protein

rplK

PMID:15690043

Experiment(s):EBI-884491

Protein

rplL

PMID:15690043

Experiment(s):EBI-884491

Protein

rplM

PMID:15690043

Experiment(s):EBI-884491

Protein

rplS

PMID:15690043

Experiment(s):EBI-884491

Protein

rplV

PMID:15690043

Experiment(s):EBI-884491

Protein

rplW

PMID:15690043

Experiment(s):EBI-884491

Protein

rpmC

PMID:15690043

Experiment(s):EBI-884491

Protein

rpsG

PMID:15690043

Experiment(s):EBI-884491

Protein

yehX

PMID:15690043

Experiment(s):EBI-884491

Protein

ygaF

PMID:15690043

Experiment(s):EBI-884491

Protein

yehX

PMID:19402753

LCMS(ID Probability):99.0

Protein

lhgO

PMID:19402753

LCMS(ID Probability):99.0

edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MAKTAAALHI LVKEEKLALD LLEQIKNGAD FGKLAKKHSI CPSGKRGGDL GEFRQGQMVP
AFDKVVFSCP VLEPTGPLHT QFGYHIIKVL YRN
Length

93

Mol. Wt

10.231 kDa

pI

9.5 (calculated)

Extinction coefficient

2,980 - 3,230 (calc based on 2 Y, 0 W, and 2 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0A9L5

Domain

9..91

PF00639 PPIC-type PPIASE domain

PMID:19920124

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ppiC taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131633

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948285

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012334

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9L5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12352

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12352

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948285

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002222

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2256

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

7.764+/-0.084

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.042704626

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

9133

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1330

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

4213

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

ppiC

edit table
Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:3957816..3957856 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3775 (EcoliWiki Page)

NCBI GEO profiles for ppiC

microarray

GenExpDB:b3775 (EcoliWiki Page)

Summary of data for ppiC from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3957344..3957658) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:F9[7]

edit table

<protect></protect>

Notes

Accessions Related to ppiC Expression

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12352

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2256

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3775

EcoGene

EcoGene:EG12352

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002222

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012334

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000013455 (score: 1.000; bootstrap: 51%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000035584 (score: 1.000; bootstrap: 62%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G26550 (score: 1.000; bootstrap: 56%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000022592 (score: 1.000; bootstrap: 50%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00039707 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00012996 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000017926 (score: 1.000; bootstrap: 53%)
  • ENSCAFP00000008331 (score: 0.900)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016451 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-1714 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-2654 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0203448 (score: 1.000; bootstrap: 55%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0015379 (score: 1.000; bootstrap: 100%)
  • FBgn0052845 (score: 0.151)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14299-PA (score: 1.000; bootstrap: 67%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000006157 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000247970 (score: 1.000; bootstrap: 52%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000017005 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000005818 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Mus musculus

  • MGI:1346036 (score: 1.000; bootstrap: 51%)

From Inparanoid:20070104

Oryza gramene

  • Q69WA8 (score: 1.000; bootstrap: 49%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000017779 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000027819 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YJR017C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC16C43 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000134102 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00015744001 (score: 1.000; bootstrap: 56%)
  • GSTENP00032632001 (score: 0.074)
  • GSTENP00012339001 (score: 0.062)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000012882 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000048869 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

G7V-669

From SHIGELLACYC

E. coli O157

G7E-2

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Panther (EcoliWiki Page)

PTHR10657:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:54534

Pfam (EcoliWiki Page)

PF00639 PPIC-type PPIASE domain

EcoCyc

EcoCyc:EG12352

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12352

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002222

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2256

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012334

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ppiC:On_One_Page&oldid=222166"