Detailed view for Tb927.9.12870

Basic information

TDR Targets ID: 18789
Trypanosoma brucei, trafficking protein particle complex subunit 1, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.3066 | Length (AA): 140 | MW (Da): 16167 | 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

PF04099   Sybindin-like family

Gene Ontology

Mouse over links to read term descriptions.
GO:0030008   TRAPP complex  
GO:0005801   cis-Golgi network  
GO:0016192   vesicle-mediated transport  
GO:0006888   ER to Golgi vesicle-mediated transport  
GO:0006810   transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 2 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
1 134 3cue (C) 1 153 30.00 0 0.98 1.28924 -0.83
2 140 2j3t (C) 2 140 32.00 0 1 1.49996 -1.46

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_128429)

Species Accession Gene Product
Arabidopsis thaliana AT1G51160   Sybindin-like domain-containing protein
Babesia bovis BBOV_IV010580   hypothetical protein
Brugia malayi Bm1_13955   trafficking protein particle complex subunit 1, putative
Candida albicans CaO19.7934   part of TRAPP (Transport Protein Particle) G890
Candida albicans CaO19.302   part of TRAPP (Transport Protein Particle) G890
Caenorhabditis elegans CELE_DC2.8   Protein DC2.8
Dictyostelium discoideum DDB_G0273579   hypothetical protein
Dictyostelium discoideum DDB_G0273467   hypothetical protein
Drosophila melanogaster Dmel_CG1359   BET5 ortholog (S. cerevisiae)
Echinococcus granulosus EgrG_000828500   Sybindin protein
Entamoeba histolytica EHI_197660   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000828500   Sybindin protein
Giardia lamblia GL50803_95269   Bet5-like protein
Homo sapiens ENSG00000170043   trafficking protein particle complex 1
Leishmania braziliensis LbrM.34.2790   hypothetical protein, conserved
Leishmania donovani LdBPK_352930.1   Sybindin-like family, putative
Leishmania infantum LinJ.35.2930   hypothetical protein, conserved
Leishmania major LmjF.35.2880   hypothetical protein, conserved
Leishmania mexicana LmxM.34.2880   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_14191   hypothetical protein
Mus musculus ENSMUSG00000049299   trafficking protein particle complex 1
Neospora caninum NCLIV_065150   sybindin-like family domain-containing protein, putative
Oryza sativa 4323988   Os01g0513700
Plasmodium berghei PBANKA_1037000   trafficking protein particle complex subunit 1, putative
Plasmodium falciparum PF3D7_1405200   trafficking protein particle complex subunit 1, putative
Plasmodium knowlesi PKNH_1352900   trafficking protein particle complex subunit 1, putative
Plasmodium vivax PVX_086175   trafficking protein particle complex subunit 1, putative
Plasmodium yoelii PY07060   unknown protein
Saccharomyces cerevisiae YML077W   Bet5p
Schistosoma mansoni Smp_041680   bet5-related
Schmidtea mediterranea mk4.006225.03   Trafficking protein particle complex subunit 1
Schmidtea mediterranea mk4.023587.01   Trafficking protein particle complex subunit 1
Trypanosoma brucei gambiense Tbg972.9.7910   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.12870   trafficking protein particle complex subunit 1, putative
Trypanosoma congolense TcIL3000_9_5370   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510659.74   Sybindin-like family, putative
Trypanosoma cruzi TcCLB.510745.30   Sybindin-like family, putative
Toxoplasma gondii TGME49_247648   Sybindin family protein
Trichomonas vaginalis TVAG_001870   bet5, putative

Essentiality

Tb927.9.12870 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.3810 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.3810 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.3810 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.3810 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YML077W Saccharomyces cerevisiae inviable yeastgenome
TGME49_247648 Toxoplasma gondii Probably essential sidik
TGME49_247648 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) 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: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain 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 Tb927.9.12870 (Trypanosoma brucei), trafficking protein particle complex subunit 1, putative
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