Detailed view for TcCLB.508277.360

Basic information

TDR Targets ID: 44067
Trypanosoma cruzi, ubiquitin hydrolase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 5.3399 | Length (AA): 1333 | MW (Da): 149733 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Pfam domains

PF00443   Ubiquitin carboxyl-terminal hydrolase
PF12436   ICP0-binding domain of Ubiquitin-specific protease 7

Gene Ontology

Mouse over links to read term descriptions.
GO:0036459   GO:thiol-dependent ubiquitinyl hydrolase activity  

GO:0016579   protein deubiquitination  
GO:0004221   ubiquitin thiolesterase activity  
GO:0006511   ubiquitin-dependent protein catabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 9 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
82 447 1vjv (A) 103 495 20.00 0 1 0.38 -0.2
97 484 2f1z (A) 223 551 38.00 0 1 0.41 0.09
6 481 2f1z (B) 110 553 29.00 0.00032 1 0.433589 0.76
80 448 1vjv (A) 104 496 22.00 0 1 0.478819 -0.01
85 814 5j7t (A) 211 881 25.00 0 1 0.560137 1.3
89 424 1vjv (A) 110 484 25.00 0.000000009 1 0.430263 0.43
89 624 5j7t (A) 215 675 38.00 0 1 0.574301 0.79
718 1309 5c56 (A) 641 1081 15.00 0 0.88 -0.026389 2.31
887 937 3gew (D) 136 192 18.00 0 0.01 0.26826 -0.71

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
Lower 20-40% 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_151295)

Species Accession Gene Product
Leishmania braziliensis LbrM.15.1240   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania donovani LdBPK_151320.1   ubiquitin hydrolase, putative
Leishmania infantum LinJ.15.1320   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania major LmjF.15.1300   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania mexicana LmxM.15.1300   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Trypanosoma brucei gambiense Tbg972.9.2940   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Trypanosoma brucei Tb927.9.5520   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma congolense TcIL3000_0_04870   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.508277.360 this record   ubiquitin hydrolase, putative

Essentiality

TcCLB.508277.360 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.4020 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4020 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.160.4020 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.4020 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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
  • 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.

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 log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or 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
Species Known druggable target Linked compounds Reference
Leishmania major ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0278 0.31 0.3356
0.034 0.327 0.3268
0.0282 0.3187 0.3187

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.

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User comments

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Gene identifier TcCLB.508277.360 (Trypanosoma cruzi), ubiquitin hydrolase, putative
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