Detailed view for Smp_123940

Basic information

TDR Targets ID: 285750
Schistosoma mansoni, xp-G/rad2 DNA repair endonuclease family
Source Database / ID:  GeneDB

pI: 4.7308 | Length (AA): 991 | MW (Da): 112081 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF00752   XPG N-terminal domain
PF00867   XPG I-region

Gene Ontology

Mouse over links to read term descriptions.
GO:0016788   hydrolase activity, acting on ester bonds  
GO:0005634   nucleus  
GO:0003824   catalytic activity  
GO:0003697   single-stranded DNA binding  
GO:0003677   DNA binding  
GO:0004519   endonuclease activity  
GO:0004518   nuclease activity  
GO:0006289   nucleotide-excision repair  
GO:0006281   DNA repair  

Metabolic Pathways

Nucleotide excision repair (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
1 88 4q0r (B) 1 771 49.00 0.12 0.99 0.373299 0.82
2 174 5t9j (A) 2 184 21.00 0.0024 0.89 0.467071 -0.16
241 665 4gmo (A) 73 602 12.00 0 0.73 0.44766 -0.09
565 816 1rxw (A) 42 310 21.00 0 1 0.307089 0.36
636 778 4q0w (A) 86 884 37.00 0 1 0.502899 0.54
658 783 4wa8 (A) 129 260 33.00 0.00000024 1 0.487744 0.22

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128675)

Species Accession Gene Product
Arabidopsis thaliana AT3G28030   DNA repair protein UVH3
Babesia bovis BBOV_II000500   Rad2 endonuclease, putative
Brugia malayi Bm1_05790   XPG N-terminal domain containing protein
Candida albicans CaO19.1324   similar to RAD13, excision repair protein
Candida albicans CaO19.8904   similar to RAD13, excision repair protein
Caenorhabditis elegans CELE_F57B10.6   Protein XPG-1
Cryptosporidium hominis Chro.40058   RAD2
Cryptosporidium parvum cgd4_440   XPG, DNA excision repair protein, flap endonuclease
Dictyostelium discoideum DDB_G0294290   xeroderma pigmentosum group G family protein
Drosophila melanogaster Dmel_CG10890   mutagen-sensitive 201
Echinococcus granulosus EgrG_000321400   DNA repair protein complementing XP G cells
Entamoeba histolytica EHI_100400   DNA-repair protein, putative
Echinococcus multilocularis EmuJ_000321400   DNA repair protein complementing XP G cells
Homo sapiens ENSG00000270181   BIVM-ERCC5 readthrough
Homo sapiens ENSG00000134899   excision repair cross-complementation group 5
Loa Loa (eye worm) LOAG_00986   hypothetical protein
Mus musculus ENSMUSG00000026048   excision repair cross-complementing rodent repair deficiency, complementation group 5
Neospora caninum NCLIV_037790   RAD2 endonuclease, putative
Oryza sativa 4331991   Os03g0205400
Plasmodium berghei PBANKA_0303700   DNA repair protein RAD2, putative
Plasmodium falciparum PF3D7_0206000   DNA repair protein RAD2, putative
Plasmodium knowlesi PKNH_0414900   DNA repair protein RAD2, putative
Plasmodium vivax PVX_003735   DNA repair protein RAD2, putative
Plasmodium yoelii PY01122   XPG I-region, putative
Saccharomyces cerevisiae YGR258C   Rad2p
Schistosoma japonicum Sjp_0023590   DNA-repair protein rad13, putative
Schistosoma mansoni Smp_123940   xp-G/rad2 DNA repair endonuclease family
Schmidtea mediterranea mk4.006295.00  
Schmidtea mediterranea mk4.005914.00  
Toxoplasma gondii TGME49_268560   XPG N-terminal domain-containing protein
Theileria parva TP04_0530   DNA repair protein rad2, putative
Theileria parva TP04_0531   hypothetical protein, conserved
Trichomonas vaginalis TVAG_046610   flap endonuclease-1, putative

Essentiality

Smp_123940 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F57B10.6 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0303700 Plasmodium berghei Dispensable plasmo
TGME49_268560 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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
Species Known druggable target Linked compounds Reference
Homo sapiens excision repair cross-complementation group 5 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0077 0.405 0.4756
0.0044 1 1
0.0044 1 1
0.0036 0.3124 0.3124
0.0044 1 1
0.0044 1 1
0.0036 1 1
0.0074 1 1
0.0173 1 1
0.0044 1 1
0.0072 0.2769 0.3729
0.004 1 1
0.0077 0.8148 1
0.0074 0.2554 0.2554
0.0044 1 1
0.0078 0.6848 0.6848
0.0044 0.5851 0.5851
0.015 1 1
0.0044 1 1
0.0163 0.2876 0.3587
0.0073 0.2579 0.2299
0.0044 1 1
0.0044 0.8175 0.8175
0.0044 1 1
0.0044 0.4298 0.4298
0.0044 1 1
0.0044 1 1

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 Smp_123940 (Schistosoma mansoni), xp-G/rad2 DNA repair endonuclease family
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