Detailed view for Tb927.11.8010

Basic information

TDR Targets ID: 11750
Trypanosoma brucei, DNA repair protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.2008 | Length (AA): 762 | MW (Da): 86555 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: | 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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain
PF13920   Zinc finger, C3HC4 type (RING finger)

Gene Ontology

Mouse over links to read term descriptions.
GO:0000113   nucleotide-excision repair factor 4 complex  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0008270   zinc ion binding  
GO:0008094   DNA-dependent ATPase activity  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0004386   helicase activity  
GO:0006281   DNA repair  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
158 742 3mwy (W) 351 902 22.00 0 1 0.696917 1.55
472 528 5aiu (A) 133 188 46.00 0.16 0.88 0.122003 1.32
475 534 5trb (A) 921 972 33.00 0 0.99 0.37494 -0.33
476 527 4ccg (X) 307 367 33.00 0 1 0.230441 0.82
476 554 2yu4 (A) 10 89 23.00 0 0.85 0.291875 0.19
539 688 2rb4 (A) 308 455 16.00 0 0.5 0.35605 -0.21
550 699 2hjv (A) 221 364 17.00 0 0.38 0.37505 -0.28
574 726 1z5z (A) 748 899 35.00 0.000000000019 1 0.408987 0.63

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_127144)

Species Accession Gene Product
Arabidopsis thaliana AT1G02670   P-loop containing nucleoside triphosphate hydrolases superfamily protein
Arabidopsis thaliana AT5G43530   Helicase protein with RING/U-box domain
Arabidopsis thaliana AT5G05130   DNA/RNA helicase
Arabidopsis thaliana AT5G22750   DNA/RNA helicase protein RAD5
Brugia malayi Bm1_31435   SNF2 family N-terminal domain containing protein
Candida albicans CaO19.2097   similar to putative RAD5 ATPase/DNA helicase (SNF2 family helicase domain)
Candida albicans CaO19.9644   similar to putative RAD5 ATPase/DNA helicase (SNF2 family helicase domain)
Caenorhabditis elegans CELE_T23H2.3   Protein T23H2.3
Caenorhabditis elegans CELE_F54E12.2   Protein F54E12.2
Dictyostelium discoideum DDB_G0272082   C3HC4-type zinc finger-containing protein
Dictyostelium discoideum DDB_G0282115   C3HC4-type zinc finger-containing protein
Dictyostelium discoideum DDB_G0281949   CHR group protein
Drosophila melanogaster Dmel_CG10445   CG10445 gene product from transcript CG10445-RD
Drosophila melanogaster Dmel_CG2684   lodestar
Echinococcus granulosus EgrG_000412300   Zinc finger RING type
Homo sapiens 8458   transcription termination factor, RNA polymerase II
Homo sapiens ENSG00000071794   helicase-like transcription factor
Leishmania braziliensis LbrM.28.2000   DNA repair protein-like protein
Leishmania braziliensis LbrM.28.0790   DNA repair protein, putative
Leishmania donovani LdBPK_281950.1   DNA repair protein-like protein
Leishmania donovani LdBPK_280810.1   DNA repair protein, putative
Leishmania infantum LinJ.28.0810   DNA repair protein, putative
Leishmania infantum LinJ.28.1950   DNA repair protein-like protein
Leishmania major LmjF.28.1830   DNA repair protein-like protein
Leishmania major LmjF.28.0760   DNA repair protein, putative
Leishmania mexicana LmxM.28.1830   DNA repair protein-like protein
Leishmania mexicana LmxM.28.0760   DNA repair protein, putative
Loa Loa (eye worm) LOAG_04901   hypothetical protein
Loa Loa (eye worm) LOAG_04903   hypothetical protein
Loa Loa (eye worm) LOAG_04902   hypothetical protein
Mus musculus ENSMUSG00000002428   helicase-like transcription factor
Mus musculus ENSMUSG00000033222   transcription termination factor, RNA polymerase II
Neospora caninum NCLIV_011070   AAR147Wp, related
Oryza sativa 4329524   Os02g0527100
Oryza sativa 4344076   Os07g0642400
Oryza sativa 4335086   Os04g0177300
Onchocerca volvulus OVOC2773   Transcription termination factor 2 homolog
Plasmodium berghei PBANKA_1356400   DNA repair protein RAD5, putative
Plasmodium falciparum PF3D7_1343400   DNA repair protein RAD5, putative
Plasmodium knowlesi PKNH_1258000   DNA repair protein RAD5, putative
Plasmodium vivax PVX_083065   DNA repair protein RAD5, putative
Plasmodium yoelii PY02949   DNA repair protein-like-related
Saccharomyces cerevisiae YLR032W   DNA helicase RAD5
Trypanosoma brucei gambiense Tbg972.11.9160   DNA repair protein, putative
Trypanosoma brucei Tb927.11.8010   DNA repair protein, putative
Trypanosoma congolense TcIL3000_0_20470   DNA repair protein, putative
Trypanosoma congolense TcIL3000.11.8530   DNA repair protein, putative
Trypanosoma cruzi TcCLB.504041.29   DNA repair protein, putative
Trypanosoma cruzi TcCLB.508815.30   DNA repair protein, putative
Toxoplasma gondii TGME49_318480   SWI2/SNF2-containing protein RAD5

Essentiality

Tb927.11.8010 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0530 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.0530 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.0530 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.0530 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F54E12.2 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_1356400 Plasmodium berghei Dispensable plasmo
TGME49_318480 Toxoplasma gondii Essentiality uncertain sidik
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.
  • 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
  • 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
  • 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
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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) 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

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.

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Gene identifier Tb927.11.8010 (Trypanosoma brucei), DNA repair protein, putative
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