Detailed view for PVX_003705

Basic information

TDR Targets ID: 268163
Plasmodium vivax, DNA-directed RNA polymerase II 16 kDa subunit, putative
Source Database / ID:  PlasmoDB 

pI: 6.2312 | Length (AA): 132 | MW (Da): 15087 | 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

PF03874   RNA polymerase Rpb4

Gene Ontology

Mouse over links to read term descriptions.
GO:0055029   nuclear DNA-directed RNA polymerase complex  
GO:0000166   nucleotide binding  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003824   catalytic activity  
GO:0044237   cellular metabolic process  
GO:0006352   transcription initiation  
GO:0006350   transcription  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
RNA polymerase (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
7 127 1wcm (D) 22 217 31.00 0 1 1.08 -0.66
8 124 2c35 (A) 16 134 32.00 0.00000000011 1 1.33 -0.7
4 129 4by7 (D) 19 219 29.00 0 0.97 1.08075 -0.38
6 131 2c35 (A) 14 141 29.00 0 0.98 1.36375 -0.6

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 - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 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_128606)

Species Accession Gene Product
Arabidopsis thaliana AT5G09920   RNA polymerase II, Rpb4, core protein
Babesia bovis BBOV_III006040   RNA polymerase Rpb4 family protein
Brugia malayi Bm1_25045   DNA-directed RNA polymerase II 16 kDa polypeptide, putative
Candida albicans CaO19.7786   similar to N terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.145   similar to C terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.146   similar to N terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.7785   similar to C terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Caenorhabditis elegans CELE_F43E2.2   Protein RPB-4
Cryptosporidium parvum cgd3_4320   conserved hypothetical protein
Dictyostelium discoideum DDB_G0282739   DNA-directed RNA polymerase II subunit 4
Drosophila melanogaster Dmel_CG43662   CG43662 gene product from transcript CG43662-RF
Echinococcus granulosus EgrG_000089400   DNA directed RNA polymerase II subunit
Echinococcus multilocularis EmuJ_000089400   DNA directed RNA polymerase II subunit
Homo sapiens ENSG00000144231   polymerase (RNA) II (DNA directed) polypeptide D
Loa Loa (eye worm) LOAG_07020   DNA-directed RNA polymerase II polypeptide
Mus musculus ENSMUSG00000024258   polymerase (RNA) II (DNA directed) polypeptide D
Neospora caninum NCLIV_031640   DNA-directed RNA polymerase II, putative
Oryza sativa 4328083   Os02g0116900
Plasmodium berghei PBANKA_0303200   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium falciparum PF3D7_0205500   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium knowlesi PKNH_0415400   DNA-directed RNA polymerase I subunit, putative
Plasmodium vivax PVX_003705   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium yoelii PY02525   RNA polymerase Rpb4
Saccharomyces cerevisiae YJL140W   DNA-directed RNA polymerase II subunit RPB4
Schistosoma japonicum Sjp_0061690   ko:K03012 DNA-directed RNA polymerase II subunit D, putative
Schistosoma mansoni Smp_074230   DNA-directed RNA polymerase II
Schmidtea mediterranea mk4.002007.01   DNA-directed RNA polymerase II subunit RPB4
Toxoplasma gondii TGME49_231380   DNA-directed RNA polymerase II RPB4
Theileria parva TP02_0359   DNA-directed RNA polymerase II subunit Rpb4, putative
Trichomonas vaginalis TVAG_183050   hypothetical protein

Essentiality

PVX_003705 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F43E2.2 Caenorhabditis elegans embryonic lethal wormbase
TGME49_231380 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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.
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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_003705 (Plasmodium vivax), DNA-directed RNA polymerase II 16 kDa subunit, putative
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