Detailed view for PVX_079985

Basic information

TDR Targets ID: 267784
Plasmodium vivax, hypothetical protein, conserved
Source Database / ID:  PlasmoDB 

pI: 7.3371 | Length (AA): 1702 | MW (Da): 193043 | 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

PF02463   RecF/RecN/SMC N terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030915   Smc5-Smc6 complex  
GO:0005694   chromosome  
GO:0005524   ATP binding  
GO:0006281   DNA repair  
GO:0000724   double-strand break repair via homologous recombination  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 16 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
266 391 1xew (X) 3 129 24.00 0.00000013 0.98 0.1 0.24
1560 1696 1xew (Y) 1012 1144 17.00 0.000000016 0.14 0.24 -0.48
15 148 2y44 (A) 58 195 11.00 0.11 0 0.204531 -0.71
266 548 3qku (A) 2 739 30.00 0.19 0.98 0.147975 0.94
266 369 1f2t (A) 2 104 31.00 0.036 0.78 0.215805 0.41
269 355 3aux (A) 7 83 40.00 0.18 0.97 0.408816 0.07
464 619 3u0r (A) 30 196 28.00 0.86 0.08 0.267357 0.1
495 637 4uos (A) 8 164 27.00 0.15 0.82 0.384719 -1.01
496 682 4tql (A) 48 231 25.00 0.01 0.94 0.378571 -0.37
569 752 4uos (A) 3 185 20.00 0.00015 0.32 0.449508 -1.82
1401 1700 3zgx (A) 52 1175 19.00 0 0.87 0.192663 0.98
1478 1686 3auy (A) 138 985 24.00 0.19 0.52 0.265497 0.37
1612 1683 1e69 (A) 1072 1139 32.00 0.17 0.3 0.321003 0.09
1619 1693 4rvc (A) 134 205 15.00 0.028 0.03 0.144866 -0.13
1624 1698 1b0u (A) 158 231 14.00 0.0000015 0.04 0.0528658 0.5
1641 1702 3aux (A) 943 999 33.00 0.036 0.51 0.247228 0.65

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 - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 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_127751)

Species Accession Gene Product
Arabidopsis thaliana AT5G61460   protein SMC6B
Arabidopsis thaliana AT5G07660   structural maintenance of chromosomes 6A
Babesia bovis BBOV_IV000980   hypothetical protein
Babesia bovis BBOV_IV000970   hypothetical protein
Brugia malayi Bm1_42705   SMC family, C-terminal domain containing protein
Candida albicans CaO19_6568   hypothetical protein
Candida albicans CaO19.6568   potential SMC chromosomal ATPase similar to S. cerevisiae RHC18 (YLR383W) nuclear DNA repair complex ATPase
Candida albicans CaO19.13921   potential SMC chromosomal ATPase similar to S. cerevisiae RHC18 (YLR383W) nuclear DNA repair complex ATPase
Caenorhabditis elegans CELE_F54D5.14   Protein SMC-6
Caenorhabditis elegans CELE_C23H4.6   Protein C23H4.6, isoform B
Cryptosporidium hominis Chro.80351   hypothetical protein
Cryptosporidium parvum cgd8_3010   Smc ABC ATpase
Dictyostelium discoideum DDB_G0288993   AAA ATPase domain-containing protein
Drosophila melanogaster Dmel_CG5524   java no jive
Entamoeba histolytica EHI_180450   structural maintenance of chromosomes protein
Entamoeba histolytica EHI_033700   RecF/RecN/SMC domain containing protein
Giardia lamblia GL50803_7648   SMC6 protein
Homo sapiens ENSG00000163029   structural maintenance of chromosomes 6
Loa Loa (eye worm) LOAG_05474   hypothetical protein
Mus musculus ENSMUSG00000020608   structural maintenance of chromosomes 6
Neospora caninum NCLIV_053750   Smc ABC ATpase, related
Oryza sativa 9267891   Os09g0121000
Onchocerca volvulus OVOC10307   Structural maintenance of chromosomes protein 6 homolog
Plasmodium berghei PBANKA_1240000   structural maintenance of chromosomes protein 6, putative
Plasmodium falciparum PF3D7_0525200   structural maintenance of chromosomes protein 6, putative
Plasmodium knowlesi PKNH_1007600   structural maintenance of chromosomes protein 6, putative
Plasmodium vivax PVX_079985   hypothetical protein, conserved
Plasmodium yoelii PY06788   hypothetical protein
Saccharomyces cerevisiae YLR383W   DNA repair protein SMC6
Toxoplasma gondii TGME49_309400   RecF/RecN/SMC N terminal domain-containing protein
Theileria parva TP01_0122   hypothetical protein
Theileria parva TP01_0120   hypothetical protein
Trichomonas vaginalis TVAG_176480   DNA repair protein Smc6

Essentiality

PVX_079985 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F54D5.14 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_1240000 Plasmodium berghei Essential plasmo
TGME49_309400 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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): 0.1

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PVX_079985 (Plasmodium vivax), hypothetical protein, conserved
Title for this comment
Comment