Detailed view for PF3D7_1348500

Basic information

TDR Targets ID: 158
Plasmodium falciparum, TBC domain protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.0822 | Length (AA): 347 | MW (Da): 41207 | 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

PF00566   Rab-GTPase-TBC domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0005097   Rab GTPase activator activity  
GO:0032313   regulation of Rab GTPase activity  

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
17 339 1fkm (A) 249 629 43.00 0 1 1.69 -2.66
17 340 1fkm (A) 249 630 42.00 0 1 1.57942 -1.63
21 339 2qfz (A) 196 508 46.00 0 1 1.53961 -1.38

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, gametocyte, early schizont. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, early trophozoite, late schizont, late trophozoite, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, late ring, Oocyst, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 16 hs, Ring, 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
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_127685)

Species Accession Gene Product
Arabidopsis thaliana AT2G30710   RabGAP/TBC domain-containing protein
Babesia bovis BBOV_II002460   TBC domain containing protein
Brugia malayi Bm1_37555   TBC domain containing protein
Candida albicans CaO19.11292   Gtpase activating protein for Ypt1p
Candida albicans CaO19.3811   Gtpase activating protein for Ypt1p
Caenorhabditis elegans CELE_F32B6.8   Protein TBC-3, isoform B
Cryptosporidium hominis Chro.30295   TBC domain
Cryptosporidium parvum cgd3_2560   TBC1 domain containing protein
Dictyostelium discoideum DDB_G0269982   hypothetical protein
Drosophila melanogaster Dmel_CG5745   CG5745 gene product from transcript CG5745-RA
Echinococcus granulosus EgrG_001054300   TBC1 domain family 2B
Entamoeba histolytica EHI_196990   Rab GTPase activating protein, putative
Echinococcus multilocularis EmuJ_001054300   TBC1 domain family 2B
Homo sapiens ENSG00000054611   TBC1 domain family, member 22A
Homo sapiens ENSG00000065491   TBC1 domain family, member 22B
Leishmania braziliensis LbrM.30.1470   GTPase activating protein, putative
Leishmania donovani LdBPK_301410.1   GTPase activating protein, putative
Leishmania infantum LinJ.30.1410   GTPase activating protein, putative
Leishmania major LmjF.30.1350   GTPase activating protein, putative
Leishmania mexicana LmxM.29.1350   GTPase activating protein, putative
Loa Loa (eye worm) LOAG_05272   TBC domain-containing protein
Mus musculus ENSMUSG00000042203   TBC1 domain family, member 22B
Mus musculus ENSMUSG00000051864   TBC1 domain family, member 22a
Neospora caninum NCLIV_014640   TBC domain-containing protein, putative
Oryza sativa 4347577   Os09g0515800
Plasmodium berghei PBANKA_1361300   TBC domain protein, putative
Plasmodium falciparum PF3D7_1348500   TBC domain protein, putative
Plasmodium knowlesi PKNH_1252400   TBC domain protein, putative
Plasmodium vivax PVX_083320   TBC domain protein, putative
Plasmodium yoelii PY05115   TBC domain, putative
Saccharomyces cerevisiae YOR070C   Gyp1p
Schistosoma japonicum Sjp_0216130   TBC1 domain family member 22B, putative
Schistosoma mansoni Smp_022130   hypothetical protein
Schmidtea mediterranea mk4.008868.00  
Schmidtea mediterranea mk4.011578.00  
Schmidtea mediterranea mk4.009193.02  
Trypanosoma brucei gambiense Tbg972.6.2600   GTPase activating protein, conserved, putative
Trypanosoma brucei Tb927.6.2830   GTPase activating protein, conserved
Trypanosoma congolense TcIL3000_0_57880   GTPase activating protein, conserved
Trypanosoma cruzi TcCLB.511753.80   GTPase activating protein, putative
Trypanosoma cruzi TcCLB.511501.50   GTPase activating protein, putative
Toxoplasma gondii TGME49_285730   TBC domain containing protein
Theileria parva TP04_0374   TBC domain protein, putative
Trichomonas vaginalis TVAG_235350   conserved hypothetical protein
Trichomonas vaginalis TVAG_329290   conserved hypothetical protein
Trichomonas vaginalis TVAG_483540   conserved hypothetical protein

Essentiality

PF3D7_1348500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.2830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.2830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.2830 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.6.2830 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_285730 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

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.

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User comments

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Gene identifier PF3D7_1348500 (Plasmodium falciparum), TBC domain protein, putative
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