Detailed view for Smp_129630

Basic information

TDR Targets ID: 290095
Schistosoma mansoni, tRNA pseudouridine synthase D
Source Database / ID:  GeneDB

pI: 8.948 | Length (AA): 540 | MW (Da): 60661 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF01142   tRNA pseudouridine synthase D (TruD)

Gene Ontology

Mouse over links to read term descriptions.
GO:0009982   pseudouridine synthase activity  
GO:0003723   RNA binding  
GO:0009451   RNA modification  
GO:0001522   pseudouridine synthesis  

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
22 538 5kkp (A) 108 648 36.00 0 1 1.18341 0.32
78 151 2qdf (A) 21 92 24.00 0 0.78 0.437337 -0.83
110 168 2cpm (A) 72 129 19.00 0 0.28 0.345559 -0.86

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_127405)

Species Accession Gene Product
Arabidopsis thaliana AT3G04820   pseudouridine synthase
Babesia bovis BBOV_I000450   tRNA pseudouridine synthase D (TruD) domain containing protein
Brugia malayi Bm1_36725   tRNA pseudouridine synthase D
Candida albicans CaO19.1753   potential pseudouridine synthase similar to S. cerevisiae PUS7 (YOR243C) which modifies the U2 snRNA GUAGUA box
Candida albicans CaO19.9322   potential pseudouridine synthase similar to S. cerevisiae PUS7 (YOR243C) which modifies the U2 snRNA GUAGUA box
Caenorhabditis elegans CELE_B0024.11   Protein B0024.11
Cryptosporidium hominis Chro.20165   hypothetical protein
Cryptosporidium parvum cgd2_1510   conserved hypothetical protein
Dictyostelium discoideum DDB_G0271632   tRNA pseudouridine synthase D
Drosophila melanogaster Dmel_CG6745   CG6745 gene product from transcript CG6745-RA
Echinococcus granulosus EgrG_000767100   tRNA pseudouridine synthase D
Entamoeba histolytica EHI_199620   tRNA pseudouridine synthase D domain-containing protein
Echinococcus multilocularis EmuJ_000767100   tRNA pseudouridine synthase D
Giardia lamblia GL50803_6702   Pseudouridylates U2 snRNA at position 35
Homo sapiens ENSG00000091127   pseudouridylate synthase 7 (putative)
Leishmania braziliensis LbrM.35.6030   hypothetical protein, conserved
Leishmania donovani LdBPK_366000.1   pseudouridine synthase TruD, putative
Leishmania infantum LinJ.36.6000   hypothetical protein, conserved
Leishmania major LmjF.36.5750   hypothetical protein, conserved
Leishmania mexicana LmxM.36.5750   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_05940   tRNA pseudouridine synthase D
Mus musculus ENSMUSG00000057541   pseudouridylate synthase 7 homolog (S. cerevisiae)
Oryza sativa 9272465   Os05g0509300
Onchocerca volvulus OVOC4561   Putative pseudouridine synthase
Plasmodium berghei PBANKA_0518800   tRNA pseudouridine synthase D, putative
Plasmodium falciparum PF3D7_1035000   U2 snRNA/tRNA pseudouridine synthase, putative
Plasmodium knowlesi PKNH_0620200   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_110975   hypothetical protein, conserved
Plasmodium yoelii PY03893   hypothetical protein
Saccharomyces cerevisiae YOR243C   pseudouridine synthase PUS7
Schistosoma japonicum Sjp_0061310   Putative pseudouridine synthase C1A4.09, putative
Schistosoma japonicum Sjp_0211170   ko:K01855 pseudouridylate synthase 7 homolog [EC:5.4.99.-], putative
Schistosoma mansoni Smp_129630   tRNA pseudouridine synthase D
Schmidtea mediterranea mk4.002683.02  
Schmidtea mediterranea mk4.011105.00   Putative pseudouridine synthase
Trypanosoma brucei gambiense Tbg972.10.11070   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.9050   pseudouridine synthase TruD, putative
Trypanosoma congolense TcIL3000_10_7820   pseudouridine synthase TruD, putative
Trypanosoma cruzi TcCLB.509795.60   pseudouridine synthase TruD, putative
Trypanosoma cruzi TcCLB.504171.59   tRNA pseudouridine synthase TruD, putative
Theileria parva TP02_0922   hypothetical protein, conserved
Trichomonas vaginalis TVAG_050450   tRNA pseudouridine synthase D, putative
Trichomonas vaginalis TVAG_350960   tRNA pseudouridine synthase D, putative

Essentiality

Smp_129630 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.9050 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.9050 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.9050 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.9050 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0518800 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

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

No literature references available for this target.

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Gene identifier Smp_129630 (Schistosoma mansoni), tRNA pseudouridine synthase D
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