Detailed view for Tb927.11.9810

Basic information

TDR Targets ID: 11351
Trypanosoma brucei, NUDIX hydrolase 3, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.8311 | Length (AA): 246 | MW (Da): 27515 | 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

PF00293   NUDIX domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0016787   hydrolase activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 4 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
4 240 3bm4 (A) 15 208 43.00 0 1 1.23651 0.2
71 214 1ktg (A) 2 136 17.00 0.000097 0.96 0.843266 -0.86
84 128 1ktg (A) 16 56 54.00 0.017 0.95 0.613027 1.08
105 144 3f13 (A) 41 81 35.00 0 0.63 0.489502 0.37

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 Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic. 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_127505)

Species Accession Gene Product
Brugia malayi Bm1_16495   ADP-sugar pyrophosphatase
Candida albicans CaO19.14088   similar to S. cerevisiae ADP-ribose pyrophosphatase (MutT/NUDIX domain)
Candida albicans CaO19.6796   similar to S. cerevisiae ADP-ribose pyrophosphatase (MutT/NUDIX domain)
Caenorhabditis elegans CELE_W02G9.1   Protein NDX-2
Dictyostelium discoideum DDB_G0282603   hypothetical protein
Escherichia coli b3397   adenosine nucleotide hydrolase
Entamoeba histolytica EHI_097930   muT/nudix family protein
Homo sapiens ENSG00000165609   nudix (nucleoside diphosphate linked moiety X)-type motif 5
Leishmania braziliensis LbrM.35.3890   nudix hydrolase-like protein
Leishmania donovani LdBPK_363840.1   NUDIX hydrolase 3, putative
Leishmania infantum LinJ.36.3840   nudix hydrolase-like protein
Leishmania major LmjF.36.3660   nudix hydrolase-like protein
Leishmania mexicana LmxM.36.3660   nudix hydrolase-like protein
Loa Loa (eye worm) LOAG_03218   ADP-sugar pyrophosphatase
Mus musculus ENSMUSG00000025817   nudix (nucleoside diphosphate linked moiety X)-type motif 5
Mycobacterium tuberculosis Rv1700   NUDIX hydrolase
Mycobacterium ulcerans MUL_1689   NUDIX hydrolase
Neospora caninum NCLIV_023800   hydrolase, NUDIX family domain containing protein, putative
Saccharomyces cerevisiae YBR111C   Ysa1p
Trypanosoma brucei gambiense Tbg972.11.11000   NUDIX hydrolase, conserved, putative
Trypanosoma brucei Tb927.11.9810   NUDIX hydrolase 3, putative
Trypanosoma congolense TcIL3000.11.10300   NUDIX hydrolase 3, putative
Trypanosoma cruzi TcCLB.511233.100   NUDIX hydrolase 3, putative
Trypanosoma cruzi TcCLB.506963.110   NUDIX hydrolase 3, putative
Toxoplasma gondii TGME49_282190   hydrolase, NUDIX family protein
Treponema pallidum TP0731   hypothetical protein
Theileria parva TP04_0755   hypothetical protein
Trichomonas vaginalis TVAG_184500   Nudix hydrolase 14, mitochondrial precursor, putative

Essentiality

Tb927.11.9810 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.1570 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.1570 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.1570 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.1570 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3397 Escherichia coli non-essential goodall
TGME49_282190 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.

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

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 Tb927.11.9810 (Trypanosoma brucei), NUDIX hydrolase 3, putative
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