Detailed view for Tb927.2.6050

Basic information

TDR Targets ID: 55274
Trypanosoma brucei, beta prime COP protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.0523 | Length (AA): 855 | MW (Da): 94486 | 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

PF00400   WD domain, G-beta repeat
PF04053   Coatomer WD associated region

Gene Ontology

Mouse over links to read term descriptions.
GO:0006890   retrograde vesicle-mediated transport, Golgi to ER  
GO:0030126   COPI vesicle coat  
GO:0030117   membrane coat  
GO:0005794   Golgi apparatus  
GO:0005515   protein binding  
GO:0005198   structural molecule activity  
GO:0016192   vesicle-mediated transport  
GO:0006886   intracellular protein transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
11 303 4j87 (A) 5 326 39.00 0 1 0.790294 -0.79
16 797 3mkq (A) 12 812 37.00 0 1 1.34406 -0.12
116 258 3fm0 (A) 30 176 34.00 0.0000000000063 1 0.576444 -0.41
634 851 5cwn (A) 3 201 19.00 0.029 0.23 0.398069 -0.31

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 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_127760)

Species Accession Gene Product
Arabidopsis thaliana AT3G15980   coatomer subunit beta'-3
Arabidopsis thaliana AT1G79990   coatomer subunit beta'-1
Arabidopsis thaliana AT1G52360   coatomer subunit beta'-2
Babesia bovis BBOV_IV005890   coatomer beta subunit, putative
Brugia malayi Bm1_39470   Probable coatomer beta' subunit
Candida albicans CaO19.10971   ER to Golgi trafficking, beta subunit of coatomer
Candida albicans CaO19.3467   ER to Golgi trafficking, beta subunit of coatomer
Caenorhabditis elegans CELE_F38E11.19   Protein F38E11.5
Cryptosporidium hominis Chro.70561   coatomer beta subunit
Cryptosporidium parvum cgd7_5010   coatomer complex beta
Dictyostelium discoideum DDB_G0278285   WD40 repeat-containing protein
Drosophila melanogaster Dmel_CG6699   Coat Protein (coatomer) beta'
Echinococcus granulosus EgrG_000262400   coatomer subunit beta'
Entamoeba histolytica EHI_004590   coatomer complex subunit, putative
Echinococcus multilocularis EmuJ_000262400   coatomer subunit beta'
Giardia lamblia GL50803_9593   Coatomer beta subunit
Homo sapiens ENSG00000184432   coatomer protein complex, subunit beta 2 (beta prime)
Leishmania braziliensis LbrM.33.3480   beta prime cop protein, putative
Leishmania donovani LdBPK_333360.1   beta prime cop protein, putative
Leishmania infantum LinJ.33.3360   beta prime cop protein, putative
Leishmania major LmjF.33.3210   beta prime cop protein, putative
Leishmania mexicana LmxM.32.3210   beta prime cop protein, putative
Loa Loa (eye worm) LOAG_04590   hypothetical protein
Mus musculus ENSMUSG00000032458   coatomer protein complex, subunit beta 2 (beta prime)
Neospora caninum NCLIV_049710   hypothetical protein
Oryza sativa 4328694   Os02g0209100
Oryza sativa 4328693   Os02g0209000
Oryza sativa 4340097   Os06g0143900
Plasmodium berghei PBANKA_0415500   coatomer subunit beta, putative
Plasmodium falciparum PF3D7_0905900   coatomer subunit beta, putative
Plasmodium knowlesi PKNH_0703600   coatomer subunit beta, putative
Plasmodium vivax PVX_098735   coatomer complex beta subunit, putative
Plasmodium yoelii PY05987   coatomer beta' subunit
Saccharomyces cerevisiae YGL137W   Sec27p
Schistosoma japonicum Sjp_0016390   Coatomer subunit beta', putative
Schistosoma japonicum Sjp_0016400   Coatomer subunit beta', putative
Schistosoma mansoni Smp_015090   coatomer beta subunit
Schmidtea mediterranea mk4.001293.04  
Schmidtea mediterranea mk4.001293.05   Coatomer subunit beta'
Schmidtea mediterranea mk4.001293.06  
Trypanosoma brucei gambiense Tbg.972.2.4230   beta prime COP protein
Trypanosoma brucei Tb927.2.6050   beta prime COP protein
Trypanosoma congolense TcIL3000_2_1670   beta prime cop protein, putative
Trypanosoma cruzi TcCLB.506815.30   beta prime cop protein, putative
Trypanosoma cruzi TcCLB.507105.10   beta prime cop protein, putative
Toxoplasma gondii TGME49_235020   COPI protein, putative
Theileria parva TP01_0394   coatomer beta subunit, putative
Trichomonas vaginalis TVAG_038030   coatomer beta subunit, putative
Trichomonas vaginalis TVAG_488010   coatomer beta subunit, putative
Trichomonas vaginalis TVAG_191610   WD-repeat protein, putative

Essentiality

Tb927.2.6050 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.6050 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.2.6050 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.2.6050 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.2.6050 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YGL137W Saccharomyces cerevisiae inviable yeastgenome
TGME49_235020 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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 procyclic forms . 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 Tb927.2.6050 (Trypanosoma brucei), beta prime COP protein
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