Detailed view for PVX_090850

Basic information

TDR Targets ID: 269985
Plasmodium vivax, FeS cluster assembly protein SufD, putative
Source Database / ID:  PlasmoDB 

pI: 8.378 | Length (AA): 1256 | MW (Da): 144189 | Paralog Number: 0

Signal peptide: Y | 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

PF01458   Uncharacterized protein family (UPF0051)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0016226   iron-sulfur cluster assembly  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
955 1236 1vh4 (A) 138 414 23.00 0 1 0.38 -0.38
408 559 2fkj (A) 113 249 28.00 0.082 0.03 0.144119 1.01
471 657 4uos (A) 1 176 18.00 0.13 0.1 0.305085 -0.79
825 1238 1vh4 (A) 9 416 18.00 0 1 0.569518 -0.08
839 1238 1vh4 (A) 41 416 23.00 0 1 0.504671 0.21

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
Mid 40-60% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, 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_132298)

Species Accession Gene Product
Arabidopsis thaliana AT1G32500   non-intrinsic ABC protein 6
Chlamydia trachomatis CT_686   iron-sulfur assembly protein SufD
Escherichia coli b1681   component of SufBCD Fe-S cluster assembly scaffold
Mycobacterium leprae ML0594   Conserved hypothetical protein
Mycobacterium tuberculosis Rv1462   Conserved hypothetical protein
Mycobacterium ulcerans MUL_1863   hypothetical protein
Neospora caninum NCLIV_034200   sufB/sufD domain-containing protein, putative
Oryza sativa 4325986   Os01g0127300
Plasmodium berghei PBANKA_0943500   FeS cluster assembly protein SufD
Plasmodium falciparum PF3D7_1103400   FeS cluster assembly protein SufD, putative
Plasmodium knowlesi PKNH_0901000   FeS cluster assembly protein SufD, putative
Plasmodium vivax PVX_090850   FeS cluster assembly protein SufD, putative
Plasmodium yoelii PY00907   Uncharacterized protein family UPF0051, putative
Toxoplasma gondii TGME49_273445   sufB/sufD domain-containing protein
Treponema pallidum TP0613   hypothetical protein

Essentiality

PVX_090850 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu1485 Mycobacterium tuberculosis essential nmpdr
b1681 Escherichia coli non-essential goodall
PBANKA_0943500 Plasmodium berghei Essential plasmo
TGME49_273445 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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.

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

User comments

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Gene identifier PVX_090850 (Plasmodium vivax), FeS cluster assembly protein SufD, putative
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