Detailed view for Tb927.6.3500

Basic information

TDR Targets ID: 11195
Trypanosoma brucei, endosomal trafficking protein RME-8, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.661 | Length (AA): 2236 | MW (Da): 253874 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF00226   DnaJ domain
PF14237   Domain of unknown function (DUF4339)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0031072   heat shock protein binding  
GO:0005488   binding  
GO:0006897   endocytosis  

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
211 956 3w3w (A) 238 1009 10.00 0 0.63 0.363231 0.6
975 1028 1wh2 (A) 16 72 20.00 0 0.96 0.33975 -0.99
1256 2220 1u6g (C) 4 1031 12.00 0 1 0.492174 0.83
1301 1353 2lo1 (A) 5 55 49.00 0.081 1 0.765103 -1.92
1316 1357 2och (A) 17 58 50.00 0.0000031 1 0.793684 -1.83
1319 1365 3ucs (C) 19 66 45.00 0.013 1 0.68092 -1.78

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 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_129678)

Species Accession Gene Product
Arabidopsis thaliana AT2G26890   gravitropism defective 2
Brugia malayi Bm1_08070   DnaJ domain containing protein
Caenorhabditis elegans CELE_F18C12.2   Protein RME-8, isoform A
Dictyostelium discoideum DDB_G0286293   hypothetical protein
Drosophila melanogaster Dmel_CG8014   Receptor mediated endocytosis 8
Echinococcus granulosus EgrG_000345600   dnaJ subfamily C 3
Entamoeba histolytica EHI_041980   hypothetical protein, conserved
Entamoeba histolytica EHI_188910   hypothetical protein, conserved
Entamoeba histolytica EHI_200560   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000345600   dnaJ subfamily C 3
Homo sapiens ENSG00000138246   DnaJ (Hsp40) homolog, subfamily C, member 13
Leishmania braziliensis LbrM.30.2160   endosomal trafficking protein RME-8, putative
Leishmania donovani LdBPK_302220.1   endosomal trafficking protein RME-8, putative
Leishmania infantum LinJ.30.2220   endosomal trafficking protein RME-8, putative
Leishmania major LmjF.30.2210   endosomal trafficking protein RME-8, putative
Leishmania mexicana LmxM.29.2210   endosomal trafficking protein RME-8, putative
Loa Loa (eye worm) LOAG_05007   hypothetical protein
Loa Loa (eye worm) LOAG_05008   hypothetical protein
Mus musculus ENSMUSG00000032560   DnaJ (Hsp40) homolog, subfamily C, member 13
Oryza sativa 4349486   Os10g0575200
Schistosoma japonicum Sjp_0002640   ko:K09533 DnaJ homolog, subfamily C, member 13, putative
Schistosoma mansoni Smp_175760   endosomal trafficking protein
Schmidtea mediterranea mk4.000044.16  
Schmidtea mediterranea mk4.000044.14   DnaJ homolog subfamily C member 13
Schmidtea mediterranea mk4.000044.12   DnaJ homolog subfamily C member 13
Schmidtea mediterranea mk4.000044.13   DnaJ homolog subfamily C member 13
Schmidtea mediterranea mk4.000044.15   DnaJ homolog subfamily C member 13
Trypanosoma brucei gambiense Tbg972.6.3250   endosomal trafficking protein RME-8, putative
Trypanosoma brucei Tb927.6.3500   endosomal trafficking protein RME-8, putative
Trypanosoma congolense TcIL3000_6_3040   endosomal trafficking protein RME-8, putative
Trypanosoma cruzi TcCLB.511511.10   endosomal trafficking protein RME-8, putative
Trypanosoma cruzi TcCLB.506941.9   endosomal trafficking protein RME-8, putative

Essentiality

Tb927.6.3500 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.3500 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.6.3500 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.3500 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.6.3500 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F18C12.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_F18C12.2 Caenorhabditis elegans larval arrest wormbase
CELE_F18C12.2 Caenorhabditis elegans larval lethal wormbase
CELE_F18C12.2 Caenorhabditis elegans slow growth wormbase
CELE_F18C12.2 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

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Gene identifier Tb927.6.3500 (Trypanosoma brucei), endosomal trafficking protein RME-8, putative
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