Detailed view for PVX_116765

Basic information

TDR Targets ID: 267645
Plasmodium vivax, variant-silencing SET protein, putative
Source Database / ID:  PlasmoDB 

pI: 8.7487 | Length (AA): 3021 | MW (Da): 334027 | 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

PF00856   SET domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0018024   histone-lysine N-methyltransferase activity  
GO:0008270   zinc ion binding  
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 10 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
2475 2725 1mvh (A) 195 461 23.00 0 1 -0.01 0.77
46 127 1g2d (C) 108 189 12.00 0.14 0 0.185943 -0.8
69 129 2lce (A) 14 74 13.00 0.48 0 0.231992 -1.23
824 940 3s6l (A) 18 132 30.00 0.099 0.49 0.327629 -0.4
1622 1730 3ult (A) 6 118 17.00 0.94 0.02 0.159881 -0.47
2328 2386 2yo0 (A) 1238 1299 42.00 0.62 0.09 0.21843 1.7
2489 2737 2r3a (A) 27 298 24.00 0.0000000063 1 0.246223 0.61
2578 2718 3f9x (A) 199 339 22.00 0.0011 0.94 0.339473 -0.54
2578 2718 4ldg (A) 121 264 18.00 0.7 0.88 0.271473 -0.42
2879 2941 1mm2 (A) 3 53 45.00 0.12 0.32 0.075754 1.87

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
Mid 40-60% 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_128830)

Species Accession Gene Product
Arabidopsis thaliana AT1G77300   histone-lysine N-methyltransferase ASHH2
Babesia bovis BBOV_III009070   SET domain containing protein
Brugia malayi Bm1_35965   SET domain containing protein
Candida albicans CaO19.9324   likely protein lysine methyltransferase similar to S. cerevisiae SET2 (YJL168C) histone lysine methyltransferase, transcriptiona
Candida albicans CaO19.1755   likely protein lysine methyltransferase similar to S. cerevisiae SET2 (YJL168C) histone lysine methyltransferase, transcriptiona
Caenorhabditis elegans CELE_K09F5.5   Protein SET-12
Caenorhabditis elegans CELE_C43E11.3   Protein MET-1, isoform B
Dictyostelium discoideum DDB_G0268132   SET domain-containing protein
Drosophila melanogaster Dmel_CG1716   CG1716 gene product from transcript CG1716-RA
Echinococcus granulosus EgrG_000452300   histone lysine N methyltransferase SETD2
Echinococcus granulosus EgrG_000674500   histone lysine N methyltransferase SETD2
Echinococcus multilocularis EmuJ_000452300   histone lysine N methyltransferase SETD2
Echinococcus multilocularis EmuJ_000674500   histone lysine N methyltransferase SETD2
Giardia lamblia GL50803_9130   Histone methyltransferase HMT1
Homo sapiens ENSG00000181555   SET domain containing 2
Loa Loa (eye worm) LOAG_03647   hypothetical protein
Mus musculus ENSMUSG00000044791   SET domain containing 2
Neospora caninum NCLIV_028480   hypothetical protein
Oryza sativa 4329647   Os02g0554000
Plasmodium falciparum PF3D7_1322100   histone-lysine N-methyltransferase SET2
Plasmodium knowlesi PKNH_1206700   histone-lysine N-methyltransferase SET2, putative
Plasmodium vivax PVX_116765   variant-silencing SET protein, putative
Saccharomyces cerevisiae YJL168C   Set2p
Schistosoma japonicum Sjp_0081690   IPR001202,WW/Rsp5/WWP,domain-containing
Schistosoma japonicum Sjp_0088390   Histone-lysine N-methyltransferase SETD2, putative
Schistosoma japonicum Sjp_0088400   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma mansoni Smp_103090   hypothetical protein
Schmidtea mediterranea mk4.000301.01   Probable histone-lysine N-methyltransferase CG1716
Toxoplasma gondii TGME49_257770   histone lysine methyltransferase SET2
Theileria parva TP04_0811   hypothetical protein

Essentiality

PVX_116765 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C43E11.3 Caenorhabditis elegans slow growth wormbase
CELE_C43E11.3 Caenorhabditis elegans sterile wormbase
TGME49_257770 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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 SET domain containing 2 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier PVX_116765 (Plasmodium vivax), variant-silencing SET protein, putative
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