Detailed view for Smp_001560

Basic information

TDR Targets ID: 294829
Schistosoma mansoni, hypothetical protein
Source Database / ID:  GeneDB

pI: 8.8665 | Length (AA): 576 | MW (Da): 67054 | 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

PF04434   SWIM zinc finger
PF13639   Ring finger domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
256 309 4xi6 (A) 79 125 43.00 0.0064 0.98 0.43195 -0.09
455 488 1rmd (A) 38 71 32.00 0 0.7 0.530328 -1.19
456 485 1iym (A) 151 179 45.00 0.93 0.71 0.522183 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_133212)

Species Accession Gene Product
Echinococcus granulosus EgrG_000856000   zinc finger RING domain containing protein 2
Echinococcus multilocularis EmuJ_000856000   zinc finger RING domain containing protein 2
Giardia lamblia GL50803_15868   Mitogen-activated protein kinase kinase kinase 1
Homo sapiens ENSG00000163012   zinc finger, SWIM-type containing 2
Leishmania braziliensis LbrM.08.0860   hypothetical protein
Leishmania donovani LdBPK_081001.1   Ring finger domain containing protein, putative
Leishmania infantum LinJ.08.1001   hypothetical protein, conserved
Leishmania major LmjF.08.1101   hypothetical protein, conserved
Leishmania mexicana LmxM.08.1091   hypothetical protein, conserved
Mus musculus ENSMUSG00000034552   zinc finger SWIM-type containing 2
Schistosoma japonicum Sjp_0113870   Zinc finger SWIM domain-containing protein 2, putative
Schistosoma mansoni Smp_001560   hypothetical protein
Schmidtea mediterranea mk4.005145.05   E3 ubiquitin-protein ligase ZSWIM2
Schmidtea mediterranea mk4.005145.04   E3 ubiquitin-protein ligase ZSWIM2
Schmidtea mediterranea mk4.000156.08   E3 ubiquitin-protein ligase ZSWIM2
Trypanosoma brucei gambiense Tbg972.5.4110   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.2920   Ring finger domain containing protein, putative
Trypanosoma congolense TcIL3000_5_2870   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.506321.270   Ring finger domain containing protein, putative
Trichomonas vaginalis TVAG_343610   conserved hypothetical protein

Essentiality

Smp_001560 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.2920 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.2920 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.2920 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.2920 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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_001560 (Schistosoma mansoni), hypothetical protein
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