Detailed view for PVX_083032

Basic information

TDR Targets ID: 830885
Plasmodium vivax, transcription activator, putative
Source Database / ID:  PlasmoDB 

pI: 8.1105 | Length (AA): 58 | MW (Da): 6690 | 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

PF03604   DNA directed RNA polymerase, 7 kDa subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
2 43 4bbr (B) 1146 1189 40.00 0.028 0.95 1.12764 0.45
5 40 3pwf (A) 129 161 42.00 0.18 0.9 0.96119 0.64
13 58 1twf (L) 25 70 39.00 0 0.89 1.1313 1.33
14 50 2lcq (A) 126 161 33.00 0.0014 0.83 0.879431 1.36

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 80-100% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intraerythrocytic - 18 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_130124)

Species Accession Gene Product
Arabidopsis thaliana AT5G41010   DNA-directed RNA polymerase NRPB12/NRPD12/NRPE12
Candida albicans CaO19.7255   DNA-directed RNA polymerase
Caenorhabditis elegans CELE_F23B2.13   Protein RPB-12
Cryptosporidium parvum cgd7_3240   transcription activator, putative
Dictyostelium discoideum DDB_G0283365   RNA polymerase I core subunit
Drosophila melanogaster Dmel_CG34186   CG34186 gene product from transcript CG34186-RA
Echinococcus granulosus EgrG_000657300   dna directed rna polymerases i ii and iii
Echinococcus multilocularis EmuJ_000657300   DNA directed RNA polymerases I, II, and III
Homo sapiens ENSG00000147669   polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa
Loa Loa (eye worm) LOAG_10524   hypothetical protein
Mus musculus ENSMUSG00000045996   polymerase (RNA) II (DNA directed) polypeptide K
Mus musculus 100862456   DNA-directed RNA polymerases I, II, and III subunit RPABC4-like
Mus musculus 102641086   DNA-directed RNA polymerases I, II, and III subunit RPABC4-like
Oryza sativa 9269422   Os01g0530366
Oryza sativa 9272152   Os05g0151800
Oryza sativa 9266234   Os07g0105100
Plasmodium berghei PBANKA_1355800   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium falciparum PF3D7_1342700   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium knowlesi PKNH_1258700   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium vivax PVX_083032   transcription activator, putative
Saccharomyces cerevisiae YHR143W-A   DNA-directed RNA polymerase core subunit RPB12
Schistosoma japonicum Sjp_0308900   ko:K03009 DNA-directed RNA Polymerase II subunit K, putative
Schistosoma mansoni Smp_132030   hypothetical protein
Schmidtea mediterranea mk4.004777.01  
Toxoplasma gondii TGME49_254140   DNA-directed RNA polymerase II RPABC4
Trichomonas vaginalis TVAG_040880   conserved hypothetical protein

Essentiality

PVX_083032 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F23B2.13 Caenorhabditis elegans embryonic lethal wormbase
CELE_F23B2.13 Caenorhabditis elegans larval arrest wormbase
CELE_F23B2.13 Caenorhabditis elegans sterile wormbase
YHR143W-A Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1355800 Plasmodium berghei Essential plasmo
TGME49_254140 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
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.

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
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_083032 (Plasmodium vivax), transcription activator, putative
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