Detailed view for TcCLB.511217.140

Basic information

TDR Targets ID: 33592
Trypanosoma cruzi, coatomer delta subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.8476 | Length (AA): 539 | MW (Da): 58400 | Paralog Number: 2

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

PF00928   Adaptor complexes medium subunit family
PF01217   Clathrin adaptor complex small chain

Gene Ontology

Mouse over links to read term descriptions.
GO:0006890   retrograde vesicle-mediated transport, Golgi to ER  
GO:0030131   clathrin adaptor complex  
GO:0030126   COPI vesicle coat  
GO:0005515   protein binding  
GO:0006886   intracellular protein transport  
GO:0006810   transport  
GO:0016192   vesicle-mediated 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
2 153 1w63 (Q) 1 149 17.00 0 0.9 0.57 -1.29
2 142 1gw5 (S) 1 142 18.00 0 0.77 0.65 -2.1
2 153 5mu7 (B) 2 151 43.00 0 1 0.924304 -1.48
292 537 4o8q (A) 267 510 30.00 0 1 0.821701 -0.61

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 metacyclic. Smircich P
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile epimastigote. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_127690)

Species Accession Gene Product
Arabidopsis thaliana AT5G05010   clathrin adaptor complexes medium subunit family protein
Babesia bovis BBOV_II001990   conserved hypothetical protein
Brugia malayi Bm1_44825   Probable coatomer delta subunit
Candida albicans CaO19.11711   delta subunit of coatomer 1
Candida albicans CaO19.4236   delta subunit of coatomer 1
Caenorhabditis elegans CELE_C13B9.3   Protein C13B9.3
Cryptosporidium hominis Chro.70331   delta-COP
Cryptosporidium parvum cgd7_2940   coatomer complex delta chain
Dictyostelium discoideum DDB_G0268702   hypothetical protein
Drosophila melanogaster Dmel_CG14813   Coat Protein (coatomer) delta
Echinococcus granulosus EgrG_000345100   coatomer subunit delta
Entamoeba histolytica EHI_126990   hypothetical protein
Entamoeba histolytica EHI_202810   coatomer subunit delta, putative
Echinococcus multilocularis EmuJ_000345100   coatomer subunit delta
Homo sapiens ENSG00000095139   archain 1
Leishmania braziliensis LbrM.16.1220   coatomer delta subunit-like protein,delta-COP, putative,delta-coat protein, putative
Leishmania donovani LdBPK_161230.1   coatomer delta subunit-like protein
Leishmania infantum LinJ.16.1230   coatomer delta subunit-like protein,delta-COP, putative,delta-coat protein, putative
Leishmania major LmjF.16.1180   coatomer delta subunit-like protein,delta-COP, putative,delta-coat protein, putative
Leishmania mexicana LmxM.16.1180   coatomer delta subunit-like protein,delta-COP, putative,delta-coat protein, putative
Loa Loa (eye worm) LOAG_07540   ARCN1 protein
Mus musculus ENSMUSG00000032096   archain 1
Neospora caninum NCLIV_005050   coatomer delta subunit, putative
Oryza sativa 4327409   Os01g0833700
Oryza sativa 9267932   Os08g0368000
Oryza sativa 4338375   Os05g0310800
Oryza sativa 4338376   Os05g0311000
Plasmodium berghei PBANKA_0913700   coatomer subunit delta, putative
Plasmodium falciparum PF3D7_1134800   coatomer subunit delta
Plasmodium knowlesi PKNH_0933000   coatomer subunit delta, putative
Plasmodium vivax PVX_092350   coatomer delta subunit, putative
Plasmodium yoelii PY00471   probable coatomer delta subunit, putative
Saccharomyces cerevisiae YFR051C   Ret2p
Schistosoma japonicum Sjp_0054880   IPR002730,Ribonuclease P, Rpp29,domain-containing
Schistosoma japonicum Sjp_0054900   Coatomer subunit delta, putative
Schistosoma mansoni Smp_139440   coatomer delta subunit
Schistosoma mansoni Smp_031860   coatomer delta subunit
Schmidtea mediterranea mk4.004387.00   Probable coatomer subunit delta
Schmidtea mediterranea mk4.003629.00   Probable coatomer subunit delta
Trypanosoma brucei gambiense Tbg972.8.5160   coatomer delta subunit, putative,delta-COP, putative,delta-coat protein, putative
Trypanosoma brucei Tb927.8.5250   delta-coat protein, putative
Trypanosoma congolense TcIL3000_8_5100   delta-coat protein, putative
Trypanosoma cruzi TcCLB.503581.39   coatomer delta subunit, putative
Trypanosoma cruzi TcCLB.511217.140   coatomer delta subunit, putative
Trypanosoma cruzi TcCLB.506573.91   coatomer delta subunit, putative
Theileria parva TP04_0333   hypothetical protein
Theileria parva TP04_0332   hypothetical protein
Trichomonas vaginalis TVAG_260660   coatomer delta subunit, putative
Trichomonas vaginalis TVAG_214630   coatomer delta subunit, putative

Essentiality

TcCLB.511217.140 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.5250 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.5250 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.5250 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.5250 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C13B9.3 Caenorhabditis elegans larval arrest wormbase
CELE_C13B9.3 Caenorhabditis elegans larval lethal wormbase
CELE_C13B9.3 Caenorhabditis elegans sterile wormbase
YFR051C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0913700 Plasmodium berghei Slow plasmo
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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

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
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus AP-2 complex subunit sigma 142 aa 19.1% 136 aa Compounds References
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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier TcCLB.511217.140 (Trypanosoma cruzi), coatomer delta subunit, putative
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