Detailed view for PVX_085070

Basic information

TDR Targets ID: 265554
Plasmodium vivax, rRNA (adenosine-2'-O-)-methyltransferase, putative
Source Database / ID:  PlasmoDB 

pI: 8.7016 | Length (AA): 2316 | MW (Da): 258217 | Paralog Number: 0

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

Druggability Group : DG1

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

PF00588   SpoU rRNA Methylase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0008173   RNA methyltransferase activity  
GO:0003723   RNA binding  
GO:0006396   RNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
2050 2315 1gz0 (A) 3 242 16.00 0 1 0.26 -0.24
2163 2316 2ha8 (A) 22 176 50.00 0 1 0.7 -1.83
1801 1924 4wik (A) 472 596 10.00 0.29 0 0.139041 -0.43
2078 2316 1ipa (A) 18 262 20.00 0 1 0.297995 0.38
2163 2316 2ha8 (A) 22 176 50.00 0 1 0.784794 -1.25

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
Lower 20-40% 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_129882)

Species Accession Gene Product
Arabidopsis thaliana AT4G17610   tRNA/rRNA methyltransferase (SpoU) family protein
Candida albicans CaO19.5038   similar to S. cerevisiae TRM3 (YDL112W) tRNA (Gm18) ribose methyltransferase
Candida albicans CaO19.12505   similar to S. cerevisiae TRM3 (YDL112W) tRNA (Gm18) ribose methyltransferase
Cryptosporidium hominis Chro.10197   hypothetical protein
Cryptosporidium hominis Chro.10198   hypothetical protein
Cryptosporidium parvum cgd1_1720   tRNA (Gm18) ribose methylase; trm3p; SpoU superfamily - SPOUT methylase
Dictyostelium discoideum DDB_G0285499   hypothetical protein
Dictyostelium discoideum DDB_G0278965   tRNA/rRNA methyltransferase SpoU family protein
Drosophila melanogaster Dmel_CG18596   CG18596 gene product from transcript CG18596-RA
Homo sapiens ENSG00000059588   TAR (HIV-1) RNA binding protein 1
Mus musculus ENSMUSG00000090290   predicted gene, 17296
Neospora caninum NCLIV_061700   RNA methyltransferase, TrmH family domain- containing protein, putative
Oryza sativa 4331280   Os03g0100500
Plasmodium berghei PBANKA_1015300   rRNA (adenosine-2'-O-)-methyltransferase, putative
Plasmodium falciparum PF3D7_1429400   rRNA (adenosine-2'-O-)-methyltransferase, putative
Plasmodium knowlesi PKNH_1329300   rRNA (adenosine-2'-O-)-methyltransferase, putative
Plasmodium vivax PVX_085070   rRNA (adenosine-2'-O-)-methyltransferase, putative
Plasmodium yoelii PY00691   hypothetical protein
Plasmodium yoelii PY06442   Saccharomyces cerevisiae ORF 2310-related
Saccharomyces cerevisiae YDL112W   Trm3p
Schmidtea mediterranea mk4.003331.03   Probable methyltransferase TARBP1
Schmidtea mediterranea mk4.003331.04   Probable methyltransferase TARBP1
Toxoplasma gondii TGME49_218580   RNA methyltransferase, TrmH family protein

Essentiality

PVX_085070 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1015300 Plasmodium berghei Dispensable plasmo
TGME49_218580 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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

Druggability index (range: 0 to 1): 0.8

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
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_085070 (Plasmodium vivax), rRNA (adenosine-2'-O-)-methyltransferase, putative
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