Detailed view for PVX_080415

Basic information

TDR Targets ID: 265972
Plasmodium vivax, ubiquitin carboxyl-terminal hydrolase 2, putative
Source Database / ID:  PlasmoDB 

pI: 6.771 | Length (AA): 1346 | MW (Da): 152744 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG5

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00443   Ubiquitin carboxyl-terminal hydrolase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016579   protein deubiquitination  
GO:0036459   GO:thiol-dependent ubiquitinyl hydrolase activity  

GO:0004221   ubiquitin thiolesterase activity  
GO:0006511   ubiquitin-dependent protein catabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 11 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
320 660 2gfo (A) 763 1100 29.00 0 1 0.42 0.4
333 515 2gfo (A) 778 956 49.00 0 1 0.71 -0.64
1073 1343 2f1z (A) 285 551 19.00 0 0.96 0.13 0.49
20 232 4mem (A) 29 232 19.00 0 1 0.305747 0.19
330 515 2hd5 (A) 212 354 39.00 0 1 0.501187 -0.06
333 516 2y6e (A) 303 482 51.00 0 1 0.769701 -0.56
761 819 4mt2 (A) 2 60 8.00 0.41 0 0.199334 -0.89
1112 1314 3mhs (A) 251 467 31.00 0 1 0.354817 1.03
1132 1314 4w4u (D) 283 467 36.00 0 1 0.301958 0.71
1241 1304 1vjv (A) 409 479 34.00 0.19 0.82 0.256548 1
1259 1312 2gfo (A) 1051 1106 48.00 0.004 1 0.559019 0.02

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_127522)

Species Accession Gene Product
Arabidopsis thaliana AT2G40930   ubiquitin-specific protease 5
Arabidopsis thaliana AT4G10570   ubiquitin-specific protease 9
Arabidopsis thaliana AT1G32850   putative ubiquitin carboxyl-terminal hydrolase 11
Arabidopsis thaliana AT5G22030   ubiquitin-specific protease 8
Arabidopsis thaliana AT4G10590   ubiquitin-specific protease 10
Candida albicans CaO19.6260   potential ubiquitin-specific protease similar to S. cerevisiae UBP12 (YJL197W)
Candida albicans CaO19.13639   potential ubiquitin-specific protease similar to S. cerevisiae UBP12 (YJL197W)
Caenorhabditis elegans CELE_H34C03.2   Protein H34C03.2
Dictyostelium discoideum DDB_G0293770   peptidase C19 family protein
Dictyostelium discoideum DDB_G0284381   peptidase C19 family protein
Echinococcus granulosus EgrG_000837800   ubiquitin carboxyl terminal hydrolase 4
Entamoeba histolytica EHI_012290   ubiquitin carboxyl-terminal hydrolase domain containing protein
Echinococcus multilocularis EmuJ_000837800   ubiquitin carboxyl terminal hydrolase 4
Homo sapiens ENSG00000135655   ubiquitin specific peptidase 15
Homo sapiens ENSG00000114316   ubiquitin specific peptidase 4 (proto-oncogene)
Homo sapiens ENSG00000102226   ubiquitin specific peptidase 11
Mus musculus ENSMUSG00000031066   ubiquitin specific peptidase 11
Mus musculus ENSMUSG00000032612   ubiquitin specific peptidase 4 (proto-oncogene)
Mus musculus ENSMUSG00000020124   ubiquitin specific peptidase 15
Neospora caninum NCLIV_024510   Ubiquitin carboxyl-terminal hydrolase (EC 3.1.2.15), related
Oryza sativa 9271724   Os11g0667400
Oryza sativa 4342448   Os07g0160000
Oryza sativa 4352817   Os12g0621000
Oryza sativa 4348153   Os10g0160000
Plasmodium berghei PBANKA_1231500   ubiquitin carboxyl-terminal hydrolase 2, putative
Plasmodium falciparum PF3D7_0516700   ubiquitin carboxyl-terminal hydrolase 2, putative
Plasmodium knowlesi PKNH_1016600   ubiquitin carboxyl-terminal hydrolase 2, putative
Plasmodium vivax PVX_080415   ubiquitin carboxyl-terminal hydrolase 2, putative
Plasmodium yoelii PY03802   similar to ubiquitin specific protease 11-related
Saccharomyces cerevisiae YJL197W   Ubp12p
Schistosoma japonicum Sjp_0212950   ko:K01072 ubiquitin thiolesterase [EC3.1.2.15], putative
Schistosoma mansoni Smp_128770   ubiquitin-specific peptidase 4 (C19 family)
Schmidtea mediterranea mk4.030472.00  
Schmidtea mediterranea mk4.005680.00  
Schmidtea mediterranea mk4.018881.00   Ubiquitin carboxyl-terminal hydrolase
Schmidtea mediterranea mk4.018881.01  
Schmidtea mediterranea mk4.001516.05  
Schmidtea mediterranea mk4.000151.14  
Schmidtea mediterranea mk4.000151.13   Ubiquitin carboxyl-terminal hydrolase
Toxoplasma gondii TGME49_263420   ubiquitin-specific protease USP4
Trichomonas vaginalis TVAG_402720   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase
Trichomonas vaginalis TVAG_120850   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase
Trichomonas vaginalis TVAG_431770   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase
Trichomonas vaginalis TVAG_353800   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase
Trichomonas vaginalis TVAG_025610   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase

Essentiality

PVX_080415 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1231500 Plasmodium berghei Slow plasmo
TGME49_263420 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Homo sapiens ubiquitin specific peptidase 4 (proto-oncogene) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0004 0.5 0.5
0.0003 0.5 0.5
0.0004 0.5 0.5
0.0004 0.5 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier PVX_080415 (Plasmodium vivax), ubiquitin carboxyl-terminal hydrolase 2, putative
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