Detailed view for PVX_000560

Basic information

TDR Targets ID: 270114
Plasmodium vivax, queuine tRNA-ribosyltransferase, putative
Source Database / ID:  PlasmoDB 

pI: 8.051 | Length (AA): 724 | MW (Da): 80047 | Paralog Number: 1

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG5

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

PF01702   Queuine tRNA-ribosyltransferase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016763   transferase activity, transferring pentosyl groups  
GO:0008479   queuine tRNA-ribosyltransferase activity  
GO:0008616   queuosine biosynthetic process  
GO:0006400   tRNA modification  

Metabolic Pathways

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

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
192 621 2ash (A) 5 362 35.00 0 1 0.81 -0.93
60 177 1fsu (A) 248 369 31.00 0.42 0.41 0.0263834 1.5
202 623 4e2v (A) 15 383 37.00 0 1 0.805273 0.3
218 621 2ash (A) 21 362 36.00 0 1 0.835411 -0.05

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 intraerythrocytic - 12 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 6 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_126946)

Species Accession Gene Product
Brugia malayi Bm1_54510   hypothetical protein
Caenorhabditis elegans CELE_ZK829.6   Protein TGT-1
Cryptosporidium hominis Chro.70102   hypothetical protein
Cryptosporidium parvum cgd7_830   queunine tRNA-ribosyltransferase
Chlamydia trachomatis CT_193   queuine tRNA ribosyltransferase
Dictyostelium discoideum DDB_G0291802   queuine tRNA-ribosyltransferase
Dictyostelium discoideum DDB_G0275613   hypothetical protein
Drosophila melanogaster Dmel_CG4947   tRNA-guanine transglycosylase
Escherichia coli b0406   tRNA-guanine transglycosylase
Echinococcus granulosus EgrG_000447200   queuine tRNA ribosyltransferase
Entamoeba histolytica EHI_035660   queuine tRNA-ribosyltransferase, putative
Echinococcus multilocularis EmuJ_000447200   queuine tRNA ribosyltransferase
Giardia lamblia GL50803_95064   tRNA-ribosyltransferase, putative
Homo sapiens ENSG00000213339   queuine tRNA-ribosyltransferase 1
Leishmania braziliensis LbrM.17.0880   queuine tRNA-ribosyltransferase
Leishmania donovani LdBPK_301800.1   queuine tRNA-ribosyltransferase, putative
Leishmania infantum LinJ.30.1800   queuine tRNA-ribosyltransferase, putative
Leishmania major LmjF.30.1800   queuine tRNA-ribosyltransferase, putative
Leishmania mexicana LmxM.29.1800   queuine tRNA-ribosyltransferase, putative
Loa Loa (eye worm) LOAG_08521   TRNA Guanine Transglycosylase family member
Mus musculus ENSMUSG00000002825   queuine tRNA-ribosyltransferase 1
Neospora caninum NCLIV_009650   queuine tRNA-ribosyltransferase, putative
Neospora caninum NCLIV_058630   queuine tRNA-ribosyltransferase, putative
Oryza sativa 4347331   Os09g0469900
Plasmodium berghei PBANKA_1455600   queuine tRNA-ribosyltransferase, putative
Plasmodium berghei PBANKA_0615100   queuine tRNA-ribosyltransferase, putative
Plasmodium falciparum PF3D7_1242200   queuine tRNA-ribosyltransferase, putative
Plasmodium falciparum PF3D7_0717400   queuine tRNA-ribosyltransferase, putative
Plasmodium knowlesi PKNH_1461500   queuine tRNA-ribosyltransferase, putative
Plasmodium knowlesi PKNH_0312400   queuine tRNA-ribosyltransferase, putative
Plasmodium vivax PVX_101010   queuine tRNA-ribosyltransferase, putative
Plasmodium vivax PVX_000560   queuine tRNA-ribosyltransferase, putative
Plasmodium yoelii PY00825   tRNA-guanine transglycosylase-related
Plasmodium yoelii PY01488   queuine tRNA-ribosyltransferase
Schistosoma japonicum Sjp_0130290   Probable queuine tRNA-ribosyltransferase, putative
Schistosoma mansoni Smp_192000   queuine tRNA-ribosyltransferase
Schmidtea mediterranea mk4.035637.00   Queuine tRNA-ribosyltransferase
Trypanosoma brucei gambiense Tbg972.6.2920   queuine tRNA-ribosyltransferase, putative
Trypanosoma brucei Tb927.6.3130   queuine tRNA-ribosyltransferase, putative
Trypanosoma congolense TcIL3000_6_2680   queuine tRNA-ribosyltransferase, putative
Trypanosoma cruzi TcCLB.507023.200   queuine tRNA-ribosyltransferase, putative
Trypanosoma cruzi TcCLB.511751.30   queuine tRNA-ribosyltransferase, putative
Toxoplasma gondii TGME49_320620   queuine tRNA ribosyl transferase
Toxoplasma gondii TGME49_316100   queuine trna-ribosyltransferase domain-containing protein
Theileria parva TP01_1072   tRNA-guanine transglycosylase, putative
Trichomonas vaginalis TVAG_478390   queuine tRNA-ribosyltransferase, putative
Trichomonas vaginalis TVAG_032760   queuine tRNA-ribosyltransferase, putative
Trichomonas vaginalis TVAG_039010   queuine tRNA-ribosyltransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0593   queuine/archaeosine tRNA-ribosyltransferase

Essentiality

PVX_000560 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.3130 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.3130 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.3130 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.6.3130 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0406 Escherichia coli non-essential goodall
PBANKA_0615100 Plasmodium berghei Dispensable plasmo
TGME49_316100 Toxoplasma gondii Essentiality uncertain sidik
TGME49_320620 Toxoplasma gondii Essentiality uncertain sidik
TGME49_316100 Toxoplasma gondii Probably non-essential sidik
TGME49_320620 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

Druggability index (range: 0 to 1): 0.6

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Homo sapiens queuine tRNA-ribosyltransferase 1 Compounds References
Zymomonas mobilis (strain ATCC 31821 / ZM4 / CP4) tRNA-guanine transglycosylase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0056 1 0.5
0.0106 0.2743 1
0.0098 0.301 1
0.0056 0.4121 1
0.0098 0.301 1

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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PVX_000560 (Plasmodium vivax), queuine tRNA-ribosyltransferase, putative
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