Detailed view for PVX_101040

Basic information

TDR Targets ID: 265600
Plasmodium vivax, rab GDP dissociation inhibitor beta, putative
Source Database / ID:  PlasmoDB 

pI: 6.9306 | Length (AA): 453 | MW (Da): 51641 | 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

PF00996   GDP dissociation inhibitor

Gene Ontology

Mouse over links to read term descriptions.
GO:0005092   GDP-dissociation inhibitor activity  
GO:0005093   Rab GDP-dissociation inhibitor activity  
GO:0043087   regulation of GTPase activity  
GO:0015031   protein transport  
GO:0007264   small GTPase mediated signal transduction  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
1 444 1d5t (A) 1 431 55.00 0 1 1.7 -1.85
3 451 1s3e (A) 3 461 12.00 0 1 0.86 -0.23
2 444 3p1w (A) 2 444 88.00 0 1 1.96252 -1.35

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_127353)

Species Accession Gene Product
Arabidopsis thaliana AT2G44100   guanosine nucleotide diphosphate dissociation inhibitor 1
Arabidopsis thaliana AT3G59920   RAB GDP dissociation inhibitor 2
Arabidopsis thaliana AT5G09550   RAB GDP-dissociation inhibitor
Babesia bovis BBOV_III001120   GDP dissociation inhibitor rabGDI, putative
Brugia malayi Bm1_08800   Rab GDP dissociation inhibitor alpha
Candida albicans CaO19.7261   similar to GDP dissociation inhibitor
Caenorhabditis elegans CELE_Y57G11C.10   Protein GDI-1, isoform C
Cryptosporidium hominis Chro.40465   hypothetical protein
Cryptosporidium parvum cgd4_4080   putative rab GDI alpha
Dictyostelium discoideum DDB_G0268034   Rab GDP dissociation inhibitor alpha
Drosophila melanogaster Dmel_CG4422   GDP dissociation inhibitor
Echinococcus granulosus EgrG_000767200   rab gdp dissociation inhibitor
Entamoeba histolytica EHI_167060   rab GDP dissociation inhibitor alpha, putative
Entamoeba histolytica EHI_164890   rab GDP dissociation inhibitor alpha, putative
Echinococcus multilocularis EmuJ_000767200   rab gdp dissociation inhibitor
Giardia lamblia GL50803_11495   Rab GDI
Homo sapiens ENSG00000057608   GDP dissociation inhibitor 2
Homo sapiens ENSG00000203879   GDP dissociation inhibitor 1
Leishmania braziliensis LbrM.29.2140   rab-GDP dissociation inhibitor, putative
Leishmania donovani LdBPK_292270.1   rab-GDP dissociation inhibitor, putative
Leishmania infantum LinJ.29.2270   rab-GDP dissociation inhibitor, putative
Leishmania major LmjF.29.2160   rab-GDP dissociation inhibitor, putative
Leishmania mexicana LmxM.08_29.2160   rab-GDP dissociation inhibitor, putative
Loa Loa (eye worm) LOAG_08943   rab GDP dissociation inhibitor alpha
Mus musculus ENSMUSG00000015291   guanosine diphosphate (GDP) dissociation inhibitor 1
Mus musculus ENSMUSG00000021218   guanosine diphosphate (GDP) dissociation inhibitor 2
Neospora caninum NCLIV_022550   GK15875, related
Oryza sativa 4338812   Os05g0418000
Oryza sativa 4332418   Os03g0277000
Oryza sativa 4342895   Os07g0271000
Oryza sativa 4338357   Os05g0304400
Plasmodium berghei PBANKA_1456200   rab specific GDP dissociation inhibitor, putative
Plasmodium falciparum PF3D7_1242800   rab specific GDP dissociation inhibitor
Plasmodium knowlesi PKNH_1462100   rabGDI protein, putative
Plasmodium vivax PVX_101040   rab GDP dissociation inhibitor beta, putative
Plasmodium yoelii PY04102   rabGDI protein
Saccharomyces cerevisiae YER136W   Gdi1p
Schistosoma japonicum Sjp_0093470   Rab GDP dissociation inhibitor alpha, putative
Schistosoma japonicum Sjp_0093460   Rab GDP dissociation inhibitor alpha, putative
Schistosoma mansoni Smp_094420   rab GDP-dissociation inhibitor
Schistosoma mansoni Smp_024520   rab GDP-dissociation inhibitor
Schmidtea mediterranea mk4.001161.09  
Trypanosoma brucei gambiense Tbg972.3.5210   RAB GDP dissociation inhibitor alpha, putative
Trypanosoma brucei Tb927.3.4680   RAB GDP dissociation inhibitor alpha, putative
Trypanosoma congolense TcIL3000_3_2890   RAB GDP dissociation inhibitor alpha, putative
Trypanosoma cruzi TcCLB.510329.60   RAB GDP dissociation inhibitor alpha, putative
Toxoplasma gondii TGME49_202380   rab GDI alpha, putative
Theileria parva TP03_0715   rab GDP dissociation inhibitor, putative
Trichomonas vaginalis TVAG_126970   RAB GDP-dissociation inhibitor, putative

Essentiality

PVX_101040 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.4680 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.4680 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.4680 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.4680 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y57G11C.10 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y57G11C.10 Caenorhabditis elegans sterile wormbase
YER136W Saccharomyces cerevisiae inviable yeastgenome
TGME49_202380 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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

Druggability index (range: 0 to 1): 0.2

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_101040 (Plasmodium vivax), rab GDP dissociation inhibitor beta, putative
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