Detailed view for PVX_092090

Basic information

TDR Targets ID: 265522
Plasmodium vivax, A/G-specific adenine glycosylase, putative
Source Database / ID:  PlasmoDB 

pI: 8.5238 | Length (AA): 613 | MW (Da): 69942 | 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

PF00730   HhH-GPD superfamily base excision DNA repair protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0003824   catalytic activity  
GO:0016787   hydrolase activity  
GO:0006284   base-excision repair  
GO:0006281   DNA repair  

Metabolic Pathways

Base excision repair (KEGG)

Structural information

Modbase 3D models:

There are 7 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
116 345 1m3q (A) 65 319 11.00 0 0.84 0.29 0.1
160 370 1kg2 (A) 1 212 31.00 0 1 0.87 -1.39
168 600 1rrq (A) 12 358 25.00 0 1 0.62 0.95
167 600 5dpk (A) 11 358 24.00 0.000000000022 1 0.650494 0.96
174 293 4g1g (B) 47 186 31.00 0.64 0.65 0.268659 1.21
375 408 2em4 (A) 5 40 12.00 0.51 0 0.301465 -2.01
383 419 2adr (A) 106 142 14.00 0.5 0 0.292359 -1.17

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. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 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_128159)

Species Accession Gene Product
Arabidopsis thaliana AT4G12740   HhH-GPD base excision DNA repair family protein
Chlamydia trachomatis CT_107   A/G-specific adenine glycosylase
Dictyostelium discoideum DDB_G0270764   A/G-specific adenine DNA glycosylase
Escherichia coli b2961   adenine DNA glycosylase
Entamoeba histolytica EHI_010700   A/G-specific adenine glycosylase, putative
Homo sapiens ENSG00000132781   mutY homolog
Leishmania braziliensis LbrM.28.2340   A/G-specific adenine glycosylase, putative
Leishmania donovani LdBPK_282290.1   A/G-specific adenine glycosylase, putative
Leishmania infantum LinJ.28.2290   A/G-specific adenine glycosylase, putative
Leishmania major LmjF.28.2140   A/G-specific adenine glycosylase, putative
Leishmania mexicana LmxM.28.2140   A/G-specific adenine glycosylase, putative
Mycobacterium leprae ML1920   PROBABLE ADENINE GLYCOSYLASE MUTY
Mus musculus ENSMUSG00000028687   mutY homolog (E. coli)
Mycobacterium tuberculosis Rv3589   Probable adenine glycosylase MutY
Mycobacterium ulcerans MUL_4165   adenine glycosylase MutY
Neospora caninum NCLIV_056760   helix-hairpin-helix motif-containing protein, putative
Oryza sativa 4351781   Os12g0211400
Plasmodium berghei PBANKA_0918700   A/G-specific adenine glycosylase, putative
Plasmodium falciparum PF3D7_1129500   A/G-specific adenine glycosylase, putative
Plasmodium knowlesi PKNH_0927500   A/G-specific adenine glycosylase, putative
Plasmodium vivax PVX_092090   A/G-specific adenine glycosylase, putative
Plasmodium yoelii PY05666   A/G-specific adenine glycosylase, putative
Schistosoma japonicum Sjp_0031390   ko:K03575 A/G-specific adenine glycosylase, putative
Schistosoma mansoni Smp_001020   DNA glycosylase
Trypanosoma brucei gambiense Tbg972.11.12830   A/G-specific adenine glycosylase, putative
Trypanosoma brucei Tb927.11.11440   A/G-specific adenine glycosylase, putative
Trypanosoma congolense TcIL3000_0_22020   A/G-specific adenine glycosylase, putative
Trypanosoma cruzi TcCLB.511803.20   A/G-specific adenine glycosylase, putative
Toxoplasma gondii TGME49_313470   helix-hairpin-helix motif domain-containing protein
Treponema pallidum TP0343   A/G-specific adenine glycosylase

Essentiality

PVX_092090 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3651 Mycobacterium tuberculosis non-essential nmpdr
Tb11.01.3270 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.3270 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.3270 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.3270 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2961 Escherichia coli non-essential goodall
PBANKA_0918700 Plasmodium berghei Dispensable plasmo
TGME49_313470 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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

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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User comments

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Gene identifier PVX_092090 (Plasmodium vivax), A/G-specific adenine glycosylase, putative
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