Detailed view for Tb927.5.2400

Basic information

TDR Targets ID: 20481
Trypanosoma brucei, Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 6.446 | Length (AA): 986 | MW (Da): 108261 | Paralog Number: 0

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

Pfam domains

PF00443   Ubiquitin carboxyl-terminal hydrolase

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 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
451 711 4fk5 (A) 137 352 29.00 0.46 0.78 0.156406 0.97
762 885 2ayn (A) 316 445 31.00 0.031 0.11 0.116461 1.41

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
Mid 40-60% 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_148470)

Species Accession Gene Product
Leishmania braziliensis LbrM.17.1200   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania donovani LdBPK_171190.1   Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative
Leishmania infantum LinJ.17.1190   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania major LmjF.17.1090   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania mexicana LmxM.17.1090   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Trypanosoma brucei gambiense Tbg972.5.3400   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Trypanosoma brucei Tb927.5.2400 this record   Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma congolense TcIL3000_5_2250   Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.507087.30   Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.511307.20   cysteine peptidase, Clan CA, family C19, putative

Essentiality

Tb927.5.2400 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.2400 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.2400 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.2400 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.2400 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
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.
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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) 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 procyclic forms . References: 21363968
cell proliferation (GO:0008283) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant 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 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
0.0234 0.2576 0.2788
0.0285 0.2698 0.2696
0.0236 0.2611 0.2611

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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User comments

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Gene identifier Tb927.5.2400 (Trypanosoma brucei), Peptidase C19, ubiquitin carboxyl-terminal hydrolase, putative
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