Detailed view for Smp_170990

Basic information

TDR Targets ID: 285059
Schistosoma mansoni, vinculin
Source Database / ID:  GeneDB

pI: 5.8228 | Length (AA): 1577 | MW (Da): 176217 | 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

PF01044   Vinculin family
PF09739   Mini-chromosome maintenance replisome factor

Gene Ontology

Mouse over links to read term descriptions.
GO:0015629   actin cytoskeleton  
GO:0005198   structural molecule activity  
GO:0003779   actin binding  
GO:0051015   actin filament binding  
GO:0007155   cell adhesion  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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 1038 6bfi (A) 3 833 30.00 0 1 0.657412 0.44
3 1031 1st6 (A) 4 1053 36.00 0 1 0.757905 0.32
45 247 1dow (A) 65 260 22.00 0.00029 1 0.479125 -0.73
467 736 5xfl (A) 364 625 15.00 0 0.96 0.381411 -0.72
492 738 1h6g (A) 383 629 18.00 0 0.94 0.359827 -0.44
515 738 1h6g (B) 416 629 23.00 0 0.98 0.383242 -0.66

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_132249)

Species Accession Gene Product
Brugia malayi Bm1_37935   vinculin
Caenorhabditis elegans CELE_ZC477.9   Protein DEB-1, isoform B
Dictyostelium discoideum DDB_G0281499   vinculin-related protein
Dictyostelium discoideum DDB_G0285939   vinculin A
Drosophila melanogaster Dmel_CG3299   Vinculin
Echinococcus granulosus EgrG_000841300   vinculin
Echinococcus multilocularis EmuJ_000841300   vinculin
Homo sapiens ENSG00000035403   vinculin
Loa Loa (eye worm) LOAG_02874   vinculin
Loa Loa (eye worm) LOAG_12033   hypothetical protein
Mus musculus ENSMUSG00000021823   vinculin
Onchocerca volvulus OVOC4296   Vinculin homolog
Schistosoma japonicum Sjp_0040370   ko:K05700 vinculin, putative
Schistosoma japonicum Sjp_0040360   Conserved hypothetical protein
Schistosoma mansoni Smp_170990   vinculin
Schmidtea mediterranea mk4.026119.00   Vinculin
Schmidtea mediterranea mk4.007186.00   Vinculin
Schmidtea mediterranea mk4.013440.00   Vinculin
Schmidtea mediterranea mk4.012305.00   Vinculin
Schmidtea mediterranea mk4.011476.00   Vinculin
Schmidtea mediterranea mk4.016301.00   Vinculin

Essentiality

Smp_170990 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_ZC477.9 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZC477.9 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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.

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_170990 (Schistosoma mansoni), vinculin
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