Detailed view for TcCLB.507009.120

Basic information

TDR Targets ID: 52843
Trypanosoma cruzi, DNA repair protein RAD2, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.3147 | Length (AA): 744 | MW (Da): 82655 | Paralog Number: 1

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

Druggability Group : DG3

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

PF00752   XPG N-terminal domain
PF00867   XPG I-region

Gene Ontology

Mouse over links to read term descriptions.
GO:0016788   hydrolase activity, acting on ester bonds  
GO:0005634   nucleus  
GO:0004519   endonuclease activity  
GO:0004518   nuclease activity  
GO:0003824   catalytic activity  
GO:0003697   single-stranded DNA binding  
GO:0003677   DNA binding  
GO:0006289   nucleotide-excision repair  
GO:0006281   DNA repair  

Metabolic Pathways

Nucleotide excision repair (KEGG)

Structural information

Modbase 3D models:

There are 8 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
15 237 1rxw (A) 12 255 22.00 0 0.89 0.45 0.35
361 636 1a76 () 2 307 18.00 0 1 0.27 -0.31
410 703 1ul1 (X) 60 343 21.00 0 1 0.37 0.81
1 298 3ory (A) 1 329 16.00 0.00000014 0.53 0.453838 0.17
2 126 5k97 (A) 2 129 35.00 0.000000023 0.56 0.295911 1.01
431 660 4q0w (A) 80 964 29.00 0 1 0.53704 0.95
440 570 2izo (A) 65 254 27.00 0 1 0.385975 1.12
459 593 5t9j (A) 114 312 41.00 0 0.99 0.418352 1.75

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 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_149909)

Species Accession Gene Product
Leishmania braziliensis LbrM.34.3550   DNA repair protein RAD2, putative
Leishmania donovani LdBPK_353640.1   DNA repair protein RAD2, putative
Leishmania infantum LinJ.35.3640   DNA repair protein RAD2, putative
Leishmania major LmjF.35.3590   DNA repair protein RAD2, putative
Leishmania mexicana LmxM.34.3590   DNA repair protein RAD2, putative
Trypanosoma brucei gambiense Tbg972.9.7010   DNA repair protein RAD2, putative
Trypanosoma brucei Tb927.9.11760   DNA repair protein RAD2, putative
Trypanosoma cruzi TcCLB.507009.120   DNA repair protein RAD2, putative
Trypanosoma cruzi TcCLB.510667.40   DNA repair protein RAD2, putative

Essentiality

TcCLB.507009.120 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2870 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.2870 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.2870 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.2870 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • 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

Druggability index (range: 0 to 1): 0.6

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.507009.120 (Trypanosoma cruzi), DNA repair protein RAD2, putative
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