Detailed view for Smp_170110

Basic information

TDR Targets ID: 284936
Schistosoma mansoni, high-density lipoprotein receptor (hdl)
Source Database / ID:  GeneDB

pI: 6.6704 | Length (AA): 733 | MW (Da): 82478 | 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

PF00013   KH domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  

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
109 273 2n8l (A) 2 179 21.00 0 1 0.465502 -0.31
132 198 2hh3 (A) 13 80 22.00 0 0.96 0.578805 -2.08
194 271 2cte (A) 8 85 36.00 0.0000016 1 0.724512 -1.68
419 481 1vig (A) 14 74 54.00 0.000000046 1 0.722048 -1.06
661 733 1we8 (A) 30 95 24.00 0.74 0.78 0.299291 -0.03

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_130001)

Species Accession Gene Product
Brugia malayi Bm1_06680   KH domain containing protein
Candida albicans CaO19.5281   mitotic chromosome transmission control
Candida albicans CaO19.12746   Mitotic chromosome transmission control
Caenorhabditis elegans CELE_C08H9.2   Protein C08H9.2, isoform B
Dictyostelium discoideum DDB_G0291059   ankyrin repeat-containing protein
Drosophila melanogaster Dmel_CG5170   Dodeca-satellite-binding protein 1
Echinococcus granulosus EgrG_000478300   high density lipoprotein receptor hdl
Echinococcus multilocularis EmuJ_000478300   high density lipoprotein receptor (hdl)
Homo sapiens ENSG00000115677   high density lipoprotein binding protein
Loa Loa (eye worm) LOAG_02848   KH domain-containing protein
Loa Loa (eye worm) LOAG_13057   hypothetical protein
Mus musculus ENSMUSG00000062791   predicted gene 382
Mus musculus ENSMUSG00000034088   high density lipoprotein (HDL) binding protein
Onchocerca volvulus OVOC9684   Vigilin homolog
Saccharomyces cerevisiae YJL080C   Scp160p
Schistosoma japonicum Sjp_0103920   Vigilin, putative
Schistosoma japonicum Sjp_0310790   Vigilin, putative
Schistosoma mansoni Smp_170110   high-density lipoprotein receptor (hdl)
Schmidtea mediterranea mk4.005785.00  
Schmidtea mediterranea mk4.001667.01   Vigilin
Schmidtea mediterranea mk4.009033.00   Vigilin
Schmidtea mediterranea mk4.025045.00  
Schmidtea mediterranea mk4.037792.01  
Schmidtea mediterranea mk4.037792.00  
Schmidtea mediterranea mk4.007962.01   High-density lipoprotein receptor
Schmidtea mediterranea mk4.019255.00   Vigilin

Essentiality

Smp_170110 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C08H9.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_C08H9.2 Caenorhabditis elegans larval arrest wormbase
CELE_C08H9.2 Caenorhabditis elegans slow growth wormbase
CELE_C08H9.2 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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_170110 (Schistosoma mansoni), high-density lipoprotein receptor (hdl)
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