Detailed view for Tb927.11.8210

Basic information

TDR Targets ID: 16093
Trypanosoma brucei, RAD50 DNA repair-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.9914 | Length (AA): 1349 | MW (Da): 152771 | Paralog Number: 2

Signal peptide: N | GPI Anchor: | 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

PF13476   AAA domain
PF13558   Putative exonuclease SbcCD, C subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0003690   double-stranded DNA binding  
GO:0030870   Mre11 complex  
GO:0005694   chromosome  
GO:0005634   nucleus  
GO:0016887   ATPase activity  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0006303   double-strand break repair via nonhomologous end joining  
GO:0006281   DNA repair  
GO:0000723   telomere maintenance  

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
1 380 5xei (A) 1 1014 25.00 0.19 1 0.32439 1.17
2 54 1e69 (A) 1 49 31.00 0.00000033 0.7 0.337388 -0.22
192 1205 1tr2 (A) 36 1060 12.00 0 1 0.754768 0.54
251 531 3o1i (A) 51 317 16.00 0 0.53 0.343402 -0.77
786 1022 5cwm (A) 4 225 31.00 0.015 0.92 0.451386 -0.34
926 1341 5dac (A) 2 1309 29.00 0 1 0.505477 0.17
1078 1340 5dac (A) 169 1308 43.00 0 1 0.673659 -0.19
1208 1322 3ozx (A) 428 532 17.00 0.00013 0.32 0.196348 -0.23

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 60-80% percentile Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile 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_127792)

Species Accession Gene Product
Arabidopsis thaliana AT2G31970   DNA repair protein RAD50
Babesia bovis BBOV_III009970   conserved hypothetical protein
Brugia malayi Bm1_51725   rad50 family protein
Candida albicans CaO19.9217   similar to S.cerervisiae RAD50 (YNL250W) protein involved in dsDNA break repair
Candida albicans CaO19.1648   similar to S. cerevisiae RAD50 (YNL250W) protein involved in dsDNA break repair
Caenorhabditis elegans CELE_T04H1.4   Protein RAD-50, isoform A
Cryptosporidium hominis Chro.10270   RAD50 DNA repair protein-related
Cryptosporidium hominis Chro.10271   RAD50
Cryptosporidium parvum cgd1_2410   RAD50
Dictyostelium discoideum DDB_G0292786   DNA recombination/repair protein
Drosophila melanogaster Dmel_CG6339   CG6339 gene product from transcript CG6339-RE
Echinococcus granulosus EgrG_000773300   dna repair protein rad50
Entamoeba histolytica EHI_079960   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000773300   dna repair protein rad50
Homo sapiens 10111   RAD50 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.28.0550   RAD50 DNA repair-like protein
Leishmania donovani LdBPK_280560.1   RAD50 DNA repair-like protein
Leishmania infantum LinJ.28.0560   RAD50 DNA repair-like protein
Leishmania major LmjF.28.0530   RAD50 DNA repair-like protein
Leishmania mexicana LmxM.28.0530   RAD50 DNA repair-like protein
Loa Loa (eye worm) LOAG_02334   rad50 family protein
Mus musculus ENSMUSG00000020380   RAD50 homolog (S. cerevisiae)
Neospora caninum NCLIV_029780   DNA repair protein RAD50, putative
Oryza sativa 4329409   Os02g0497500
Plasmodium berghei PBANKA_0104600   DNA repair protein RAD50, putative
Plasmodium falciparum PF3D7_0605800   DNA repair protein RAD50, putative
Plasmodium knowlesi PKNH_1144400   DNA repair protein RAD50, putative
Plasmodium vivax PVX_113460   DNA repair protein RAD50, putative
Plasmodium yoelii PY00626   unnamed protein product
Saccharomyces cerevisiae YNL250W   Rad50p
Schistosoma japonicum Sjp_0009740   DNA repair protein RAD50, putative
Schistosoma japonicum Sjp_0079430   ko:K01554 RAD50 homolog [EC:3.6.-.-], putative
Schistosoma mansoni Smp_127050   DNA repair protein RAD50
Schmidtea mediterranea mk4.018177.00   DNA repair protein rad-50
Schmidtea mediterranea mk4.011527.01   DNA repair protein rad-50
Schmidtea mediterranea mk4.010022.01   Rad50-like protein
Schmidtea mediterranea mk4.009021.00   DNA repair protein rad-50
Trypanosoma brucei gambiense Tbg972.11.9380   RAD50 DNA repair-like protein, putative
Trypanosoma brucei Tb11.v5.0573   RAD50 DNA repair-like protein, putative
Trypanosoma brucei Tb11.v5.0572   RAD50 DNA repair-like protein, putative
Trypanosoma brucei Tb927.11.8210   RAD50 DNA repair-like protein
Trypanosoma congolense TcIL3000.11.8750   RAD50 DNA repair-like protein
Trypanosoma cruzi TcCLB.508817.70   DNA repair protein RAD50, putative
Trypanosoma cruzi TcCLB.503799.10   DNA repair protein RAD50, putative
Toxoplasma gondii TGME49_257180   RecF/RecN/SMC N terminal domain-containing protein
Theileria parva TP02_0154   RAD50 DNA repair protein, putative
Trichomonas vaginalis TVAG_332600   DNA repair protein Rad50

Essentiality

Tb927.11.8210 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0340 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.0340 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.0340 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.0340 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T04H1.4 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0104600 Plasmodium berghei Dispensable plasmo
TGME49_257180 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) 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: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
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 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 contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Druggability index (range: 0 to 1): 0.1

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

1 literature reference was collected for this gene.

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

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Tb927.11.8210 (Trypanosoma brucei), RAD50 DNA repair-like protein
Title for this comment
Comment