Detailed view for PVX_113520

Basic information

TDR Targets ID: 268230
Plasmodium vivax, MYND finger protein, putative
Source Database / ID:  PlasmoDB 

pI: 5.3965 | Length (AA): 479 | MW (Da): 55344 | Paralog Number: 0

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

PF01753   MYND finger

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  

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
393 447 2d8q (A) 4 58 38.00 0.000000027 0.73 0.46 1.07
32 219 4uos (A) 2 183 8.00 0.022 0 0.433184 -0.55
323 364 3wdf (A) 17 56 40.00 0.57 0.27 0.271483 1.84
407 478 3qww (A) 22 93 26.00 0.00013 0.4 0.469813 -0.27
419 476 2dj8 (A) 1 55 40.00 0.00015 0.79 0.491886 0.49
439 478 5ccl (A) 49 90 43.00 0.00092 0.54 0.486007 0.24

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 - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 24 hs, intraerythrocytic - 30 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 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_130443)

Species Accession Gene Product
Drosophila melanogaster Dmel_CG11253   ZMYND10 homolog
Echinococcus granulosus EgrG_000463700   zinc finger MYND domain containing protein
Echinococcus multilocularis EmuJ_000463700   zinc finger MYND domain containing protein
Giardia lamblia GL50803_17543   Zinc finger domain
Homo sapiens ENSG00000004838   zinc finger, MYND-type containing 10
Leishmania braziliensis LbrM.28.0530   hypothetical protein, conserved
Leishmania donovani LdBPK_280540.1   hypothetical protein, conserved
Leishmania infantum LinJ.28.0540   hypothetical protein, conserved
Leishmania major LmjF.28.0510   hypothetical protein, conserved
Leishmania mexicana LmxM.28.0510   hypothetical protein, conserved
Mus musculus ENSMUSG00000010044   zinc finger, MYND domain containing 10
Neospora caninum NCLIV_045210   zinc finger MYND domain-containing protein, putative
Plasmodium berghei PBANKA_0105700   MYND-type zinc finger protein, putative
Plasmodium falciparum PF3D7_0607100   MYND-type zinc finger protein, putative
Plasmodium knowlesi PKNH_1143200   MYND-type zinc finger protein, putative
Plasmodium vivax PVX_113520   MYND finger protein, putative
Plasmodium yoelii PY00650   hypothetical protein
Schistosoma japonicum Sjp_0077270   Zinc finger MYND domain-containing protein 10, putative
Schistosoma japonicum Sjp_0077280   ko:K06045 squalene-hopene cyclase [EC5.4.99.17], putative
Schistosoma mansoni Smp_135930   hypothetical protein
Schmidtea mediterranea mk4.000253.00  
Trypanosoma brucei gambiense Tbg972.11.9410   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.8230   hypothetical protein, conserved
Trypanosoma congolense TcIL3000.11.8770   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.506165.10   hypothetical protein, conserved
Toxoplasma gondii TGME49_228220   MYND finger domain-containing protein
Trichomonas vaginalis TVAG_126130   zinc finger protein MYND domain-containing protein, putative
Trichomonas vaginalis TVAG_506870   zinc finger protein MYND domain-containing protein, putative

Essentiality

PVX_113520 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0320 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.0320 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.0320 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.01.0320 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0105700 Plasmodium berghei Dispensable plasmo
TGME49_228220 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
  • 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
  • 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.
  • 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
  • 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)

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 PVX_113520 (Plasmodium vivax), MYND finger protein, putative
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