Detailed view for PF3D7_0106800

Basic information

TDR Targets ID: 3189
Plasmodium falciparum, ras-related protein Rab-5C
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.2396 | Length (AA): 214 | MW (Da): 24301 | 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

PF00071   Ras family

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0005525   GTP binding  
GO:0005515   protein binding  
GO:0003924   GTPase activity  
GO:0006886   intracellular protein transport  
GO:0015031   protein transport  
GO:0007264   small GTPase mediated signal transduction  
GO:0007165   signal transduction  
GO:0006913   nucleocytoplasmic transport  

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
22 191 1r2q (A) 15 184 61.00 0 1 1.63 -2.03
22 211 2bcg (Y) 3 192 35.00 0 1 1.34 -1.19
22 210 2bcg (Y) 3 185 38.00 0.0000087 1 1.41998 -0.97
23 191 1r2q (A) 16 184 62.00 0 1 1.63952 -1.47
25 190 1ek0 (A) 5 173 60.00 0 1 1.5919 -1.34
26 189 2efe (B) 9 172 58.00 0.000000000011 1 1.57816 -1.49

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 - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, early schizont, late schizont, late trophozoite, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, gametocyte, early trophozoite, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. Lasonder E
Show/Hide expression data references
  • 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.
  • 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.

Orthologs

Ortholog group members (OG5_126724)

Species Accession Gene Product
Arabidopsis thaliana AT3G54840   Rab-like GTP-ase
Arabidopsis thaliana AT5G45130   Ras-related protein RABF2a
Arabidopsis thaliana AT4G19640   Rab5 GTPase-like protein Ara7
Babesia bovis BBOV_IV002910   Ras-related protein Rab-5
Brugia malayi Bm1_36215   Ras-related protein Rab-5B
Candida albicans CaO19.6364   similar to S. cerevisiae VPS21 (YOR089C) Rab5-like GTPase involved in vacuolar protein sorting
Candida albicans CaO19.7216   one of two genes similar to S. cerevisiae VPT52 (YKR014C) rab5-like GTPase involved in vacuolar protein sorting and endocytosis
Candida albicans CaO19.13721   similar to S. cerevisiae VPS21 (YOR089C) Rab5-like GTPase involved in vacuolar protein sorting
Candida albicans CaO19.8221   similar to S. cerevisiae VPS21 (YOR089C) Rab5-like GTPase involved in vacuolar protein sorting
Candida albicans CaO19.589   similar to S. cerevisiae VPS21 (YOR089C) Rab5-like GTPase involved in vacuolar protein sorting
Caenorhabditis elegans CELE_F26H9.6   Protein RAB-5
Cryptosporidium hominis Chro.30357   Rab5
Cryptosporidium parvum cgd3_3150   Rab5 like small GTpase
Dictyostelium discoideum DDB_G0271984   Rab GTPase
Drosophila melanogaster Dmel_CG3664   CG3664 gene product from transcript CG3664-RC
Echinococcus granulosus EgrG_000990600   ras protein rab
Entamoeba histolytica EHI_026420   Rab family GTPase
Entamoeba histolytica EHI_117960   Rab family GTPase
Echinococcus multilocularis EmuJ_000990600   ras protein rab
Homo sapiens ENSG00000111540   RAB5B, member RAS oncogene family
Homo sapiens ENSG00000108774   RAB5C, member RAS oncogene family
Homo sapiens ENSG00000124209   RAB22A, member RAS oncogene family
Homo sapiens ENSG00000144566   RAB5A, member RAS oncogene family
Leishmania braziliensis LbrM.29.2670   hypothetical protein, conserved
Leishmania braziliensis LbrM.18.1230   ras-related protein rab-5, putative
Leishmania donovani LdBPK_130220.1   ras-related protein RAB5B, putative
Leishmania donovani LdBPK_181140.1   Ras-related protein Rab5A, putative
Leishmania infantum LinJ.13.0220   small Rab GTP binding protein, putative
Leishmania infantum LinJ.18.1140   ras-related protein rab-5, putative
Leishmania major LmjF.13.0220   small Rab GTP binding protein, putative
Leishmania major LmjF.18.1130   ras-related protein rab-5, putative
Leishmania mexicana LmxM.18.1130   ras-related protein rab-5, putative
Leishmania mexicana LmxM.13.0220   small Rab GTP binding protein, putative
Loa Loa (eye worm) LOAG_01129   Rab5
Mus musculus ENSMUSG00000019173   RAB5C, member RAS oncogene family
Mus musculus ENSMUSG00000000711   RAB5B, member RAS oncogene family
Mus musculus 19334   RAB22A, member RAS oncogene family
Mus musculus ENSMUSG00000017831   RAB5A, member RAS oncogene family
Neospora caninum NCLIV_038540   RAB22A, member RAS oncogene family, related
Oryza sativa 4352862   Os12g0631100
Oryza sativa 4331646   Os03g0151900
Oryza sativa 4341888   Os06g0687100
Oryza sativa 4333662   Os03g0666500
Oryza sativa 4348725   Os10g0441800
Plasmodium berghei PBANKA_0206500   ras-related protein Rab-5C, putative
Plasmodium falciparum PF3D7_0106800   ras-related protein Rab-5C
Plasmodium knowlesi PKNH_0206700   ras-related protein Rab-5C, putative
Plasmodium vivax PVX_081430   ras-related protein Rab-5C, putative
Plasmodium yoelii PY01029   Rab5c GTPase-related
Saccharomyces cerevisiae YOR089C   Rab family GTPase VPS21
Saccharomyces cerevisiae YKR014C   Rab family GTPase YPT52
Schistosoma japonicum Sjp_0035820   ko:K07888 Ras-related protein Rab-5B, putative
Schistosoma mansoni Smp_040570.1   rab5
Schistosoma mansoni Smp_040570.2   rab5
Schmidtea mediterranea mk4.001933.02   Drab5
Schmidtea mediterranea mk4.001858.07   Ras-related protein Rab-30
Schmidtea mediterranea mk4.008787.00   Ras-related protein Rab-17
Schmidtea mediterranea mk4.095075.00  
Trypanosoma brucei gambiense Tbg972.11.5230   small GTPase, putative,small GTP-binding protein Rab5b, putative
Trypanosoma brucei gambiense Tbg972.10.15640   ras-related protein rab-5,GTP binding protein, putative
Trypanosoma brucei Tb927.10.12960   Ras-related protein Rab5A
Trypanosoma brucei Tb927.11.4570   Ras-related protein Rab5B
Trypanosoma congolense TcIL3000.11.4670   ras-related protein RAB5B, putative
Trypanosoma congolense TcIL3000_10_11060   Ras-related protein Rab5A, putative
Trypanosoma cruzi TcCLB.509805.60   Ras-related protein Rab5A, putative
Trypanosoma cruzi TcCLB.511269.4   Ras-related protein Rab5A, putative
Trypanosoma cruzi TcCLB.506227.180   ras-related protein RAB5B, putative
Toxoplasma gondii TGME49_267810   Rab 5
Theileria parva TP01_0639   GTP-binding protein rab5, putative
Trichomonas vaginalis TVAG_424920   RAB 3 and, putative
Trichomonas vaginalis TVAG_470600   GTP-binding protein ypt10, putative
Trichomonas vaginalis TVAG_060820   RAB, putative
Trichomonas vaginalis TVAG_300910   Rabx18 protein, putative
Trichomonas vaginalis TVAG_044270   RAB, putative
Trichomonas vaginalis TVAG_498380   Rab20, putative
Trichomonas vaginalis TVAG_052730   Rabx20 protein, putative
Trichomonas vaginalis TVAG_388290   RAB, putative
Trichomonas vaginalis TVAG_368730   Rab12, putative
Trichomonas vaginalis TVAG_081590   Rab5b, putative
Trichomonas vaginalis TVAG_423520   RAB, putative
Trichomonas vaginalis TVAG_008100   Rabx38 protein, putative
Trichomonas vaginalis TVAG_340860   Rab7g protein, putative
Trichomonas vaginalis TVAG_489360   Rab7g protein, putative
Trichomonas vaginalis TVAG_000080   RAB 3 and, putative
Trichomonas vaginalis TVAG_038190   small GTPase rabi, putative
Trichomonas vaginalis TVAG_106390   RAB-36 and, putative
Trichomonas vaginalis TVAG_320300   GTP-binding protein Rab2, putative
Trichomonas vaginalis TVAG_119750   Rab17, putative
Trichomonas vaginalis TVAG_222450   Rabx18 protein, putative

Essentiality

PF3D7_0106800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.12960 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.12960 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.12960 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.10.12960 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.02.2160 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.2160 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.2160 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.02.2160 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F26H9.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_F26H9.6 Caenorhabditis elegans larval arrest wormbase
CELE_F26H9.6 Caenorhabditis elegans larval lethal wormbase
CELE_F26H9.6 Caenorhabditis elegans sterile wormbase
PBANKA_0206500 Plasmodium berghei Dispensable plasmo
TGME49_267810 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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_0106800 (Plasmodium falciparum), ras-related protein Rab-5C
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