Detailed view for PVX_094915

Basic information

TDR Targets ID: 265648
Plasmodium vivax, GDP-L-fucose synthase, putative
Source Database / ID:  PlasmoDB 

pI: 6.7479 | Length (AA): 343 | MW (Da): 39626 | 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

PF01370   NAD dependent epimerase/dehydratase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0009226   nucleotide-sugar biosynthetic process  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0050662   coenzyme binding  
GO:0016491   oxidoreductase activity  
GO:0008152   metabolic process  
GO:0044237   cellular metabolic process  

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
1 326 1ek6 (A) 1 329 16.00 0 1 1.04 -0.72
2 326 1e6u (A) 3 304 23.00 0 1 1.15 -0.84
3 326 1kew (A) 1 326 18.00 0 1 1.24 -0.81
1 37 1ek6 (A) 1 37 27.00 0.14 0.05 0.302272 0.39
3 49 2ydy (A) 29 93 32.00 0.8 0.36 0.517426 -0.66
4 343 4e5y (A) 9 321 39.00 0 1 1.36915 -0.28

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
Lower 20-40% percentile intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intraerythrocytic - 6 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_129198)

Species Accession Gene Product
Arabidopsis thaliana AT1G73250   GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase 1
Arabidopsis thaliana AT1G17890   putative GDP-L-fucose synthase 2
Brugia malayi Bm1_11280   GDP-L-fucose synthetase
Caenorhabditis elegans CELE_R01H2.5   Protein GER-1
Dictyostelium discoideum DDB_G0270184   hypothetical protein
Drosophila melanogaster Dmel_CG3495   GDP-4-keto-6-deoxy-D-mannose 3,5-epimerase/4-reductase
Escherichia coli b2052   bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase/GDP-4-dehydro-6-L-deoxygalactose reductase
Echinococcus granulosus EgrG_000476900   GDP L fucose synthase
Echinococcus multilocularis EmuJ_000476900   GDP L fucose synthase
Homo sapiens ENSG00000104522   tissue specific transplantation antigen P35B
Loa Loa (eye worm) LOAG_04263   hypothetical protein
Mus musculus ENSMUSG00000022570   tissue specific transplantation antigen P35B
Mycobacterium tuberculosis Rv1512   Probable nucleotide-sugar epimerase EpiA
Neospora caninum NCLIV_014250   NAD-dependent epimerase/dehydratase, related
Oryza sativa 4341699   Os06g0652400
Onchocerca volvulus OVOC13467  
Plasmodium berghei PBANKA_1212400   GDP-L-fucose synthase, putative
Plasmodium falciparum PF3D7_1014000   GDP-L-fucose synthase
Plasmodium knowlesi PKNH_0813800   GDP-L-fucose synthase, putative
Plasmodium vivax PVX_094915   GDP-L-fucose synthase, putative
Plasmodium yoelii PY01921   transplantation antigen p35b-related
Schistosoma japonicum Sjp_0050740   ko:K02377 GDP-L-fucose synthase [EC1.1.1.271], putative
Schistosoma mansoni Smp_104720   NAD dependent epimerase/dehydratase
Schmidtea mediterranea mk4.013198.00   Probable GDP-L-fucose synthase
Schmidtea mediterranea mk4.004837.00   Probable GDP-L-fucose synthase
Trypanosoma brucei gambiense Tbg972.11.15620   GDP-L-fucose synthetase, putative
Trypanosoma brucei Tb927.11.13990   GDP-L-fucose synthetase
Trypanosoma congolense TcIL3000.11.14350   GDP-L-fucose synthetase, putative
Trypanosoma cruzi TcCLB.511727.300   GDP-L-fucose synthetase, putative
Toxoplasma gondii TGME49_286220   GDP-L-fucose synthetase

Essentiality

PVX_094915 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.5560 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.5560 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5560 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5560 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2052 Escherichia coli non-essential goodall
PBANKA_1212400 Plasmodium berghei Dispensable plasmo
TGME49_286220 Toxoplasma gondii Probably non-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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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

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_094915 (Plasmodium vivax), GDP-L-fucose synthase, putative
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