Detailed view for Tb927.9.11930

Basic information

TDR Targets ID: 16776
Trypanosoma brucei, DNA-repair protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.9913 | Length (AA): 768 | MW (Da): 85703 | Paralog Number: 0

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

PF03835   Rad4 transglutaminase-like domain
PF10403   Rad4 beta-hairpin domain 1
PF10405   Rad4 beta-hairpin domain 3

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0005634   nucleus  
GO:0003684   damaged DNA binding  
GO:0003677   DNA binding  
GO:0006289   nucleotide-excision repair  

Metabolic Pathways

Nucleotide excision repair (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
176 720 2qsf (A) 157 630 20.00 0 1 0.528235 1.33
432 628 2au3 (A) 56 241 28.00 0.059 0.96 0.35871 0.55

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, 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_128561)

Species Accession Gene Product
Arabidopsis thaliana AT5G16630   DNA repair protein Rad4
Brugia malayi Bm1_35290   DNA repair protein Rad4 containing protein
Brugia malayi Bm1_03115   DNA repair protein Rad4 containing protein
Candida albicans CaO19.14014   similar to S. cerevisiae repairosome nucleotide excision repair protein.
Candida albicans CaO19.6722   similar to S. cerevisiae repairosome nucleotide excision repair protein.
Caenorhabditis elegans CELE_Y76B12C.2   Protein XPC-1
Dictyostelium discoideum DDB_G0292296   DNA repair protein Rad4 family protein
Drosophila melanogaster Dmel_CG8153   mutagen-sensitive 210
Echinococcus granulosus EgrG_000642500   nucleotide excision repair protein
Echinococcus multilocularis EmuJ_000642500   nucleotide excision repair protein
Homo sapiens ENSG00000154767   xeroderma pigmentosum, complementation group C
Leishmania braziliensis LbrM.34.3360   DNA-repair protein, putative
Leishmania donovani LdBPK_353500.1   DNA-repair protein, putative
Leishmania infantum LinJ.35.3500   DNA-repair protein, putative
Leishmania major LmjF.35.3450   DNA-repair protein, putative
Leishmania mexicana LmxM.34.3450   DNA-repair protein, putative
Loa Loa (eye worm) LOAG_03859   DNA repair protein Rad4 containing protein
Loa Loa (eye worm) LOAG_10204   hypothetical protein
Loa Loa (eye worm) LOAG_01614   DNA repair protein Rad4 containing protein
Mus musculus ENSMUSG00000030094   xeroderma pigmentosum, complementation group C
Neospora caninum NCLIV_012740   DNA repair protein, putative
Oryza sativa 4345619   Os08g0427500
Onchocerca volvulus OVOC11468   Alkylated DNA repair protein alkB homolog
Saccharomyces cerevisiae YER162C   Rad4p
Schistosoma japonicum Sjp_0001750   DNA-repair protein complementing XP-C cells homolog, putative
Schistosoma mansoni Smp_021550   DNA repair protein xp-C / rad4
Schmidtea mediterranea mk4.003016.04   Putative dna repair protein xp-C / rad4
Schmidtea mediterranea mk4.002462.01   Putative dna repair protein xp-C / rad4
Trypanosoma brucei gambiense Tbg972.9.7210   DNA-repair protein, putative
Trypanosoma brucei Tb927.9.11930   DNA-repair protein, putative
Trypanosoma congolense TcIL3000_9_4920   DNA-repair protein, putative
Trypanosoma cruzi TcCLB.507011.140   DNA-repair protein, putative
Trypanosoma cruzi TcCLB.510665.40   DNA-repair protein, putative

Essentiality

Tb927.9.11930 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.3040 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.3040 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.3040 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.3040 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.

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 3 days). References: 21363968
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 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss 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 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
Species Target Length Identity Alignment span Linked Drugs Reference
Sus scrofa Group VII phospholipase A2 92 aa 26.7% 75 aa Compounds References
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.

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Gene identifier Tb927.9.11930 (Trypanosoma brucei), DNA-repair protein, putative
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