Detailed view for Tb927.7.6450

Basic information

TDR Targets ID: 18686
Trypanosoma brucei, tRNA-dihydrouridine synthase 3, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.4328 | Length (AA): 528 | MW (Da): 59182 | 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

PF01207   Dihydrouridine synthase (Dus)

Gene Ontology

Mouse over links to read term descriptions.
GO:0017150   tRNA dihydrouridine synthase activity  
GO:0003824   catalytic activity  
GO:0050660   FAD binding  
GO:0008152   metabolic process  
GO:0008033   tRNA processing  
GO:0055114   oxidation reduction  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 3 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
164 478 4xp7 (A) 10 324 25.00 0 1 0.742291 -0.01
167 439 1vhn (A) 6 271 30.00 0 1 0.901045 -0.63
239 446 4bfa (A) 82 280 32.00 0.0000000001 1 0.520939 1.04

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 80-100% percentile Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_127309)

Species Accession Gene Product
Arabidopsis thaliana AT4G38890   tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
Brugia malayi Bm1_16415   dihydrouridine synthase domain containing protein
Candida albicans CaO19.9138   potential tRNA dihydrouridine synthase similar to S. cerevisiae DUS3 (YLR401C)
Candida albicans CaO19.1565   potential tRNA dihydrouridine synthase similar to S. cerevisiae DUS3 (YLR401C)
Caenorhabditis elegans CELE_Y37E11B.5   Protein Y37E11B.5
Cryptosporidium hominis Chro.50134   hypothetical protein
Cryptosporidium parvum cgd5_2440   Ylr401cp-like protein with 2 CCCH domains plus Dus1p tRNA dihydrouridine synthase Tim barrel
Chlamydia trachomatis CT_644   tRNA-dihydrouridine synthase
Dictyostelium discoideum DDB_G0292686   CCCH-type zinc finger-containing protein
Drosophila melanogaster Dmel_CG10463   CG10463 gene product from transcript CG10463-RA
Escherichia coli b3260   tRNA-dihydrouridine synthase B
Entamoeba histolytica EHI_140340   hypothetical protein, conserved
Giardia lamblia GL50803_3565   Dihydrouridine synthase, putative
Homo sapiens ENSG00000141994   dihydrouridine synthase 3-like (S. cerevisiae)
Leishmania braziliensis LbrM.17.0330   hypothetical protein, conserved
Leishmania donovani LdBPK_170400.1   dihydrouridine synthase (Dus), putative
Leishmania infantum LinJ.17.0400   hypothetical protein, conserved
Leishmania major LmjF.17.0350   hypothetical protein, conserved
Leishmania mexicana LmxM.17.0350   hypothetical protein, conserved
Mycobacterium leprae ML2186   POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN
Mus musculus ENSMUSG00000007603   dihydrouridine synthase 3-like (S. cerevisiae)
Mycobacterium tuberculosis Rv0823c   Possible transcriptional regulatory protein
Mycobacterium ulcerans MUL_0444   transcriptional regulator
Neospora caninum NCLIV_045330   Dihydrouridine synthase, related
Oryza sativa 4334955   Os04g0117600
Onchocerca volvulus OVOC9137  
Saccharomyces cerevisiae YLR401C   Dus3p
Schmidtea mediterranea mk4.000116.07   tRNA-dihydrouridine(47) synthase
Trypanosoma brucei gambiense Tbg972.7.7460   tRNA-dihydrouridine synthase 3, putative
Trypanosoma brucei Tb927.7.6450   tRNA-dihydrouridine synthase 3, putative
Trypanosoma congolense TcIL3000_7_5350   tRNA-dihydrouridine synthase 3, putative
Trypanosoma cruzi TcCLB.510053.70   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.511321.20   hypothetical protein, conserved
Toxoplasma gondii TGME49_228080   dihydrouridine synthase (dus) protein
Treponema pallidum TP0980   histidine phosphokinase/phophatase (ntrB)
Trichomonas vaginalis TVAG_243820   tRNA-dihydrouridine synthase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0462   tRNA-dihydrouridine synthase

Essentiality

Tb927.7.6450 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu839 Mycobacterium tuberculosis non-essential nmpdr
Tb927.7.6450 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.6450 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.6450 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.6450 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3260 Escherichia coli non-essential goodall
TGME49_228080 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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) 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.

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User comments

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Gene identifier Tb927.7.6450 (Trypanosoma brucei), tRNA-dihydrouridine synthase 3, putative
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