Detailed view for PVX_079930

Basic information

TDR Targets ID: 269497
Plasmodium vivax, WD domain, G-beta repeat domain containing protein
Source Database / ID:  PlasmoDB 

pI: 9.322 | Length (AA): 329 | MW (Da): 36871 | Paralog Number: 1

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

PF12894   Anaphase-promoting complex subunit 4 WD40 domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 6 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
2 323 1nex (B) 364 715 13.00 0 1 1.07 0.39
7 306 1got (B) 44 340 13.00 0 1 1.12 -0.45
31 138 4d6v (A) 29 139 30.00 1 0.86 0.672367 -0.06
32 134 2pbi (B) 120 227 34.00 0.0013 0.99 0.55817 0.36
35 260 3dm0 (A) 1080 1321 25.00 0.09 1 0.83703 0.62
67 167 2ovr (B) 2384 2478 31.00 0.54 0.88 0.646091 -0.29

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. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_127408)

Species Accession Gene Product
Arabidopsis thaliana AT2G26460   RNA splicing protein SMU2
Arabidopsis thaliana AT2G34260   protein WDR55
Babesia bovis BBOV_III011140   hypothetical protein
Babesia bovis BBOV_III004110   hypothetical protein
Brugia malayi Bm1_57320   Suppressor of mec and unc defects protein
Brugia malayi Bm1_46415   hypothetical protein
Caenorhabditis elegans CELE_Y49F6B.4   Protein SMU-2
Caenorhabditis elegans CELE_Y44F5A.1   Protein Y44F5A.1
Cryptosporidium parvum cgd7_170   hypothetical protein
Dictyostelium discoideum DDB_G0282573   WD40 repeat-containing protein
Dictyostelium discoideum DDB_G0272070   hypothetical protein
Drosophila melanogaster Dmel_CG18005   CG18005 gene product from transcript CG18005-RA
Drosophila melanogaster Dmel_CG14722   CG14722 gene product from transcript CG14722-RA
Echinococcus granulosus EgrG_001058800   Protein Red
Echinococcus granulosus EgrG_000344200   WD repeat containing protein 55
Entamoeba histolytica EHI_006060   WD domain containing protein
Echinococcus multilocularis EmuJ_000344200   WD repeat containing protein 55
Echinococcus multilocularis EmuJ_001058800   Protein Red
Homo sapiens 54853   WD repeat domain 55
Homo sapiens ENSG00000113141   IK cytokine, down-regulator of HLA II
Leishmania braziliensis LbrM.35.4960   hypothetical protein, conserved
Leishmania donovani LdBPK_364940.1   hypothetical protein, conserved
Leishmania infantum LinJ.36.4940   hypothetical protein, conserved
Leishmania major LmjF.36.4710   hypothetical protein, conserved
Leishmania mexicana LmxM.36.4710   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_01901   hypothetical protein
Loa Loa (eye worm) LOAG_06696   hypothetical protein
Mus musculus ENSMUSG00000042660   WD repeat domain 55
Mus musculus ENSMUSG00000024474   IK cytokine
Neospora caninum NCLIV_065560   hypothetical protein
Neospora caninum NCLIV_018010   hypothetical protein
Oryza sativa 4344178   Os07g0660700
Oryza sativa 4351481   Os12g0143400
Oryza sativa 4349762   Os11g0146700
Onchocerca volvulus OVOC8855   3E324 homolog
Plasmodium berghei PBANKA_1241100   WD repeat-containing protein, putative
Plasmodium berghei PBANKA_1405300   RED-like protein, putative
Plasmodium falciparum PF3D7_1306800   RED-like protein, putative
Plasmodium falciparum PF3D7_0526300   WD repeat-containing protein, putative
Plasmodium knowlesi PKNH_1006500   WD repeat-containing protein, putative
Plasmodium knowlesi PKNH_1407100   RED-like protein, putative
Plasmodium vivax PVX_122175   hypothetical protein, conserved
Plasmodium vivax PVX_079930   WD domain, G-beta repeat domain containing protein
Plasmodium yoelii PY05613   hypothetical protein
Plasmodium yoelii PY03863   unnamed protein product
Schistosoma japonicum Sjp_0302480   IPR001680,WD-40 repeat;IPR011046,WD40-like,domain-containing
Schistosoma japonicum Sjp_0080930   Protein Red, putative
Schistosoma mansoni Smp_164290.1   hypothetical protein
Schistosoma mansoni Smp_164290.2   hypothetical protein
Schistosoma mansoni Smp_004480   red protein (ik factor) (cytokine ik)
Schmidtea mediterranea mk4.000935.00  
Schmidtea mediterranea mk4.038544.01   Red protein
Trypanosoma brucei gambiense Tbg972.10.12300   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.10070   hypothetical protein, conserved
Trypanosoma congolense TcIL3000_10_8320   WD domain, G-beta repeat, putative
Trypanosoma cruzi TcCLB.508307.130   hypothetical protein, conserved
Toxoplasma gondii TGME49_243240   WD domain, G-beta repeat-containing protein
Toxoplasma gondii TGME49_249360   RED family protein
Theileria parva TP03_0035   hypothetical protein
Theileria parva TP02_0734   hypothetical protein
Theileria parva TP03_0034   hypothetical protein
Trichomonas vaginalis TVAG_074040   WD-repeat protein, putative

Essentiality

PVX_079930 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.10070 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.10070 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.10070 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.10.10070 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y49F6B.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y44F5A.1 Caenorhabditis elegans slow growth wormbase
PBANKA_1405300 Plasmodium berghei Essential plasmo
TGME49_243240 Toxoplasma gondii Probably essential sidik
TGME49_249360 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • 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.
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

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 IK cytokine, down-regulator of HLA II 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_079930 (Plasmodium vivax), WD domain, G-beta repeat domain containing protein
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