Detailed view for PF3D7_0419600

Basic information

TDR Targets ID: 3968
Plasmodium falciparum, ran-specific GTPase-activating protein 1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.6332 | Length (AA): 280 | MW (Da): 33196 | 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

PF00638   RanBP1 domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005525   GTP binding  
GO:0003924   GTPase activity  
GO:0046907   intracellular transport  
GO:0006260   DNA replication  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 9 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
20 153 1k5d (B) 27 163 51.00 0 1 1.03 -0.21
33 155 1xke (A) 2 124 42.00 0 1 0.79 -0.33
17 153 5cll (B) 15 152 50.00 0 1 1.07959 -0.59
17 155 1k5d (B) 24 165 46.00 0 1 0.977729 0
33 155 4l6e (A) 2925 3047 42.00 0 1 0.984286 -0.87
33 155 1xke (A) 2 124 43.00 0 1 0.908286 -0.01
116 263 4uos (A) 27 176 26.00 0.086 0.32 1.02257 -2.54
163 222 3k29 (A) 90 149 33.00 0.14 0.02 0.996286 -4.62
189 277 3qrx (A) 63 161 31.00 0.88 0.05 0.759857 -2.49

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 intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, Sporozoite. Otto TD Zanghi G
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127714)

Species Accession Gene Product
Arabidopsis thaliana AT5G58590   Ran-binding protein 1
Arabidopsis thaliana AT1G07140   Ran-binding protein 1-a
Arabidopsis thaliana AT2G30060   Ran-binding protein 1-b
Babesia bovis BBOV_II004260   ran binding-like protein 1
Brugia malayi Bm1_09710   RanBP1 domain containing protein
Candida albicans CaO19.7477   similar to S. cerevisiae YRB1 (YDR002W) RanGTP binding protein
Caenorhabditis elegans CELE_F59A2.1   Protein NPP-9, isoform A
Cryptosporidium hominis Chro.50456   Ran-binding protein
Cryptosporidium parvum cgd5_3950   Ran-binding protein
Dictyostelium discoideum DDB_G0287391   Ran binding protein 1 domain-containing protein
Echinococcus granulosus EgrG_000906500   E3 SUMO protein ligase RanBP2
Echinococcus granulosus EgrG_001100900   Ran specific GTPase activating protein
Entamoeba histolytica EHI_185290   Ran GTPase-activating protein, putative
Echinococcus multilocularis EmuJ_001100900   Ran specific GTPase activating protein
Giardia lamblia GL50803_16969   RAN binding protein 1
Homo sapiens ENSG00000099901   RAN binding protein 1
Leishmania braziliensis LbrM.13.1240   Ran-binding protein 1, putative
Leishmania donovani LdBPK_131530.1   Ran-binding protein 1, putative
Leishmania infantum LinJ.13.1530   Ran-binding protein 1, putative
Leishmania major LmjF.13.1480   Ran-binding protein 1, putative
Leishmania mexicana LmxM.13.1480   Ran-binding protein 1, putative
Loa Loa (eye worm) LOAG_04279   hypothetical protein
Loa Loa (eye worm) LOAG_13273   hypothetical protein
Mus musculus 19385   RAN binding protein 1
Neospora caninum NCLIV_000280   RanBP1 domain containing protein, related
Oryza sativa 4332513   Os03g0292800
Oryza sativa 4338501   Os05g0350600
Plasmodium berghei PBANKA_0721700   ran-specific GTPase-activating protein 1, putative
Plasmodium falciparum PF3D7_0419600   ran-specific GTPase-activating protein 1, putative
Plasmodium knowlesi PKNH_0512300   ran-specific GTPase-activating protein 1, putative
Plasmodium vivax PVX_090070   ran binding protein 1, putative
Plasmodium yoelii PY07276   Ran-binding protein
Saccharomyces cerevisiae YDR002W   Yrb1p
Schistosoma japonicum Sjp_0077690   Ran-specific GTPase-activating protein, putative
Schistosoma japonicum Sjp_0088510   E3 SUMO-protein ligase RanBP2, putative
Schistosoma japonicum Sjp_0086550   expressed protein
Schistosoma mansoni Smp_016410   ran-binding protein
Schmidtea mediterranea mk4.006294.06  
Schmidtea mediterranea mk4.000167.18  
Trypanosoma brucei gambiense Tbg972.11.3820   Ran-binding protein 1, putative
Trypanosoma brucei Tb927.11.3380   Ran-binding protein 1, putative
Trypanosoma congolense TcIL3000.11.3270   Ran-binding protein 1, putative
Trypanosoma cruzi TcCLB.507099.30   Ran-binding protein 1, putative
Toxoplasma gondii TGME49_293340   ran binding family protein 1, putative
Theileria parva TP04_0179   ran binding protein, putative
Trichomonas vaginalis TVAG_337260   ran-binding protein, putative

Essentiality

PF3D7_0419600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.0870 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.0870 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.0870 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.0870 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F59A2.1 Caenorhabditis elegans embryonic lethal wormbase
YDR002W Saccharomyces cerevisiae inviable yeastgenome
TGME49_293340 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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.

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Gene identifier PF3D7_0419600 (Plasmodium falciparum), ran-specific GTPase-activating protein 1, putative
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