Detailed view for Smp_020540.1

Basic information

TDR Targets ID: 283500
Schistosoma mansoni, pinch
Source Database / ID:  GeneDB

pI: 8.2047 | Length (AA): 251 | MW (Da): 29408 | Paralog Number: 1

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

PF00412   LIM domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
5 44 1x63 (A) 32 71 25.00 0.042 0.95 0.472863 -0.08
5 44 1x61 (A) 22 61 33.00 0.39 1 0.564863 -0.15
111 174 1nyp (A) 3 66 61.00 0 1 0.85398 0.62
116 237 4kfz (A) 30 154 25.00 0.00044 1 0.648156 0.85

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_130503)

Species Accession Gene Product
Brugia malayi Bm1_30785   LIM protein
Caenorhabditis elegans CELE_F14D12.2   Protein UNC-97
Dictyostelium discoideum DDB_G0284863   LIM-type zinc finger-containing protein
Drosophila melanogaster Dmel_CG7954   steamer duck
Echinococcus granulosus EgrG_000195700   LIM and senescent cell antigen containing
Entamoeba histolytica EHI_001070   LIM zinc finger domain containing protein
Echinococcus multilocularis EmuJ_000195700   LIM and senescent cell antigen containing
Homo sapiens ENSG00000072163   LIM and senescent cell antigen-like domains 2
Homo sapiens ENSG00000169756   LIM and senescent cell antigen-like domains 1
Loa Loa (eye worm) LOAG_03488   hypothetical protein
Loa Loa (eye worm) LOAG_09885   LIM protein
Mus musculus ENSMUSG00000024395   LIM and senescent cell antigen like domains 2
Mus musculus ENSMUSG00000019920   LIM and senescent cell antigen-like domains 1
Onchocerca volvulus OVOC5371   Pinch, putative homolog
Schistosoma japonicum Sjp_0201350   LIM domain-containing protein unc-97, putative
Schistosoma japonicum Sjp_0120070   IPR001781,LIM, zinc-binding,domain-containing
Schistosoma japonicum Sjp_0104230   LIM domain-containing protein unc-97, putative
Schistosoma mansoni Smp_020540.1   pinch
Schistosoma mansoni Smp_020540.2   pinch
Schmidtea mediterranea mk4.014206.01   Pinch, putative

Essentiality

Smp_020540.1 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F14D12.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_F14D12.2 Caenorhabditis elegans larval lethal wormbase
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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_020540.1 (Schistosoma mansoni), pinch
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