Detailed view for Tb927.4.3110

Basic information

TDR Targets ID: 10578
Trypanosoma brucei, tRNA-dihydrouridine synthase 4, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.9514 | Length (AA): 419 | MW (Da): 45356 | 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:0003824   catalytic activity  
GO:0050660   FAD binding  
GO:0017150   tRNA dihydrouridine synthase activity  
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 6 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
2 320 2rdu (A) 17 360 14.00 0 0.87 0.824937 0.51
58 357 4xp7 (A) 11 327 21.00 0.0002 1 0.89309 0.1
196 410 4d8a (B) 40 247 17.00 0 0.77 0.567726 0.61
205 271 1h1y (A) 24 90 18.00 0 0.74 0.424505 -0.32
205 299 3qja (A) 78 167 16.00 0 0.36 0.38233 -0.37
233 283 5lsm (A) 198 247 38.00 0.11 0.99 0.578718 -0.04

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
NA% 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_129532)

Species Accession Gene Product
Brugia malayi Bm1_02480   tRNA-dihydrouridine synthase 4
Candida albicans CaO19.966   potential tRNA dihydrouridine synthase similar to S. cerevisiae DUS4 (YLR405W)
Candida albicans CaO19.8581   potential tRNA dihydrouridine synthase similar to S. cerevisiae DUS4 (YLR405W)
Caenorhabditis elegans CELE_C45G9.2   Protein C45G9.2
Dictyostelium discoideum DDB_G0291360   tRNA-dihydrouridine synthase 4-like protein
Drosophila melanogaster Dmel_CG10495   CG10495 gene product from transcript CG10495-RA
Escherichia coli b2140   tRNA-dihydrouridine synthase C
Echinococcus granulosus EgrG_000685700   tRNA dihydrouridine synthase 4
Echinococcus multilocularis EmuJ_000685700   tRNA dihydrouridine synthase 4
Homo sapiens ENSG00000105865   dihydrouridine synthase 4-like (S. cerevisiae)
Leishmania braziliensis LbrM.20.1170   hypothetical protein, conserved
Leishmania donovani LdBPK_341220.1   dihydrouridine synthase (Dus), putative
Leishmania infantum LinJ.34.1220   hypothetical protein, conserved
Leishmania major LmjF.34.1140   hypothetical protein, conserved
Leishmania mexicana LmxM.33.1140   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_06685   tRNA-dihydrouridine synthase 4
Mus musculus ENSMUSG00000020648   dihydrouridine synthase 4-like (S. cerevisiae)
Saccharomyces cerevisiae YLR405W   Dus4p
Schistosoma japonicum Sjp_0062930   ko:K05545 tRNA-dihydrouridine synthase 4, putative
Schistosoma mansoni Smp_026700   tRNA-dihydrouridine synthase
Schmidtea mediterranea mk4.000109.14   tRNA-dihydrouridine synthase
Trypanosoma brucei gambiense Tbg972.4.3120   tRNA-dihydrouridine synthase 4, putative
Trypanosoma brucei Tb927.4.3110   tRNA-dihydrouridine synthase 4, putative
Trypanosoma congolense TcIL3000_4_2920   tRNA-dihydrouridine synthase 4, putative
Trypanosoma cruzi TcCLB.506265.180   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.506435.200   hypothetical protein, conserved

Essentiality

Tb927.4.3110 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.3110 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.3110 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.3110 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.3110 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2140 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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.
  • 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 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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Gene identifier Tb927.4.3110 (Trypanosoma brucei), tRNA-dihydrouridine synthase 4, putative
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