Detailed view for TcCLB.503713.20

Basic information

TDR Targets ID: 38543
Trypanosoma cruzi, Sedlin, N-terminal conserved region, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.7272 | Length (AA): 129 | MW (Da): 14808 | Paralog Number: 1

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

PF04628   Sedlin, N-terminal conserved region

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
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 3 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
2 128 2j3w (A) 7 137 27.00 0 1 1.3548 -0.85
22 129 2j3t (D) 105 210 14.00 0 0.14 0.820509 0.52
59 124 5x9y (C) 230 298 41.00 0.82 0.55 0.683128 0.14

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 epimastigote, metacyclic. 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_128381)

Species Accession Gene Product
Arabidopsis thaliana AT1G80500   SNARE-like protein
Babesia bovis BBOV_III006610   sedlin, N-terminal conserved region family protein
Brugia malayi Bm1_15595   hypothetical protein
Candida albicans CaO19.10824   vesicular transport
Candida albicans CaO19.3314   vesicular transport
Caenorhabditis elegans CELE_W05H7.3   Protein SEDL-1
Cryptosporidium parvum cgd8_5070   hypothetical protein
Dictyostelium discoideum DDB_G0282887   trafficking protein particle complex subunit 2
Drosophila melanogaster Dmel_CG5161   TRAPP subunit 20 ortholog (S. cerevisiae)
Echinococcus granulosus EgrG_000950800   trafficking protein particle complex subunit
Echinococcus granulosus EgrG_000949710   trafficking protein particle complex 2
Entamoeba histolytica EHI_122820   sedlin, putative
Echinococcus multilocularis EmuJ_000950800   trafficking protein particle complex 2
Homo sapiens ENSG00000196459   trafficking protein particle complex 2
Loa Loa (eye worm) LOAG_02117   SEDL-1 protein
Mus musculus 66226   trafficking protein particle complex 2
Mus musculus ENSMUSG00000007777   RIKEN cDNA 0610009B22 gene
Neospora caninum NCLIV_005950   trafficking protein particle complex protein, putative
Oryza sativa 4336326   Os04g0503800
Oryza sativa 4329971   Os02g0613600
Plasmodium berghei PBANKA_1347100   trafficking protein particle complex subunit 2, putative
Plasmodium falciparum PF3D7_1332300   trafficking protein particle complex subunit 2, putative
Plasmodium knowlesi PKNH_1268300   trafficking protein particle complex subunit 2, putative
Plasmodium vivax PVX_082545   trafficking protein particle complex subunit 2, putative
Plasmodium yoelii PY05729   hypothetical protein
Saccharomyces cerevisiae YBR254C   Trs20p
Schistosoma japonicum Sjp_0307120   Trafficking protein particle complex subunit 2, putative
Schistosoma mansoni Smp_168330   mbp-1 interacting protein-2a
Schmidtea mediterranea mk4.003108.02   Probable trafficking protein particle complex subunit 2
Schmidtea mediterranea mk4.029366.00   Probable trafficking protein particle complex subunit 2
Trypanosoma brucei gambiense Tbg972.8.5900   hypothetical protein, conserved
Trypanosoma brucei Tb927.8.5900   Sedlin, N-terminal conserved region, putative
Trypanosoma cruzi TcCLB.503945.30   Sedlin, N-terminal conserved region, putative
Trypanosoma cruzi TcCLB.503713.20   Sedlin, N-terminal conserved region, putative
Toxoplasma gondii TGME49_222920   mbp-1 interacting protein-2a family protein
Theileria parva TP02_0313   hypothetical protein, conserved
Trichomonas vaginalis TVAG_308100   mbp-1 interacting protein-2A, putative
Trichomonas vaginalis TVAG_136560   mbp-1 interacting protein-2A, putative

Essentiality

TcCLB.503713.20 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
YBR254C Saccharomyces cerevisiae inviable yeastgenome
TGME49_222920 Toxoplasma gondii Probably essential sidik
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.
  • 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
  • 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
  • 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
  • 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

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.

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.503713.20 (Trypanosoma cruzi), Sedlin, N-terminal conserved region, putative
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