Detailed view for LmjF.36.6070

Basic information

TDR Targets ID: 25147
Leishmania major, rab-like GTPase activating protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.972 | Length (AA): 498 | MW (Da): 56536 | 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 5 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
196 475 1fkm (A) 249 626 25.00 0 1 0.74 -1.44
172 473 4p17 (A) 10 304 27.00 0 1 0.900626 -0.45
200 488 3qye (A) 769 1061 31.00 0 1 1.05952 -1.25
203 488 3hzj (A) 511 793 35.00 0.000000000018 1 1.1046 -1.41
212 456 3qyb (A) 894 1146 37.00 0 1 0.942368 -0.67

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 amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_127661)

Species Accession Gene Product
Arabidopsis thaliana AT3G02460   RabGAP/TBC domain-containing protein
Arabidopsis thaliana AT5G15930   plant adhesion molecule 1
Babesia bovis BBOV_II000300   TBC domain containing protein
Candida albicans CaO19.5340   similar to S. cerevisiae YPL249C
Candida albicans CaO19.12800   similar to S. cerevisiae YPL249C
Caenorhabditis elegans CELE_T24D11.1   Protein TBC-4
Cryptosporidium hominis Chro.40223   hypothetical protein
Cryptosporidium parvum cgd4_1980   TBC domain containing protein
Dictyostelium discoideum DDB_G0278181   RabGAP/TBC domain-containing protein
Dictyostelium discoideum DDB_G0276961   RabGAP/TBC domain-containing protein
Dictyostelium discoideum DDB_G0287379   RabGAP/TBC domain-containing protein
Drosophila melanogaster Dmel_CG11727   Ecotropic viral integration site 5 ortholog (H. sapiens)
Echinococcus granulosus EgrG_000703800   ecotropic viral integration site
Entamoeba histolytica EHI_010690   Rab GTPase activating protein, putative
Echinococcus multilocularis EmuJ_000703800   ecotropic viral integration site
Homo sapiens ENSG00000142459   ecotropic viral integration site 5-like
Homo sapiens ENSG00000067208   ecotropic viral integration site 5
Leishmania braziliensis LbrM.35.6380   rab-like GTPase activating protein, putative
Leishmania donovani LdBPK_366330.1   rab-like GTPase activating protein, putative
Leishmania infantum LinJ.36.6330   rab-like GTPase activating protein, putative
Leishmania major LmjF.36.6070   rab-like GTPase activating protein, putative
Leishmania mexicana LmxM.36.6070   rab-like GTPase activating protein, putative
Loa Loa (eye worm) LOAG_06176   hypothetical protein
Loa Loa (eye worm) LOAG_13893   hypothetical protein
Mus musculus ENSMUSG00000011832   ecotropic viral integration site 5 like
Mus musculus ENSMUSG00000011831   ecotropic viral integration site 5
Neospora caninum NCLIV_061510   TBC1 domain family, member 10C, related
Oryza sativa 4345560   Os08g0412600
Onchocerca volvulus OVOC3280  
Plasmodium berghei PBANKA_1341300   GTPase-activating protein, putative
Plasmodium knowlesi PKNH_1202500   GTPase-activating protein, putative
Plasmodium vivax PVX_116570   GTPase-activating protein, putative
Plasmodium yoelii PY01735   plant adhesion molecule 1-related
Saccharomyces cerevisiae YPL249C   Gyp5p
Schistosoma japonicum Sjp_0032080   Ecotropic viral integration site 5 protein homolog, putative
Schistosoma japonicum Sjp_0124870   IPR000195,RabGAP/TBC,domain-containing
Schistosoma mansoni Smp_070310   ecotropic viral integration site
Schmidtea mediterranea mk4.004630.03   Ecotropic viral integration site 5 ortholog
Schmidtea mediterranea mk4.004630.00   Ecotropic viral integration site 5 ortholog
Schmidtea mediterranea mk4.037277.00  
Schmidtea mediterranea mk4.004630.01   Ecotropic viral integration site 5 ortholog
Schmidtea mediterranea mk4.000164.02  
Schmidtea mediterranea mk4.038784.00   Ecotropic viral integration site 5 ortholog
Trypanosoma brucei gambiense Tbg972.10.10660   GTPase activating protein, putative
Trypanosoma brucei Tb11.v5.0452   GTPase activating protein, putative
Trypanosoma brucei Tb927.10.8770   disgorgin, putative
Trypanosoma congolense TcIL3000_10_7540   GTPase activating protein, putative
Trypanosoma cruzi TcCLB.508723.80   disgorgin, putative
Trypanosoma cruzi TcCLB.509789.50   rab-like GTPase activating protein, putative
Toxoplasma gondii TGME49_218870   TBC domain-containing protein
Trichomonas vaginalis TVAG_416490   ecotropic viral integration site, putative
Trichomonas vaginalis TVAG_186160   gh regulated tbc protein-1, putative

Essentiality

LmjF.36.6070 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.8770 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.8770 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.8770 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.8770 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_218870 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • 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
  • 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

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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User comments

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Gene identifier LmjF.36.6070 (Leishmania major), rab-like GTPase activating protein, putative
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