Detailed view for Smp_120440.2

Basic information

TDR Targets ID: 286523
Schistosoma mansoni, nucleic acid binding
Source Database / ID:  GeneDB

pI: 7.1343 | Length (AA): 254 | MW (Da): 29359 | Paralog Number: 2

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

PF13532   2OG-Fe(II) oxygenase superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0055114   oxidation reduction  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 2 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
11 239 3tht (A) 131 336 33.00 0.0000000028 0.99 0.925275 0.59
13 188 3dkq (A) 0 165 15.00 0 0.94 0.795813 0.25

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_129632)

Species Accession Gene Product
Arabidopsis thaliana AT4G20350   oxidoreductase
Caenorhabditis elegans CELE_B0564.2   Protein B0564.2
Cryptosporidium parvum cgd3_990   CG6144-like AlkB
Dictyostelium discoideum DDB_G0288517   hypothetical protein
Drosophila melanogaster Dmel_CG6144   CG6144 gene product from transcript CG6144-RB
Echinococcus granulosus EgrG_000841800   nucleic acid binding
Echinococcus multilocularis EmuJ_000841800   nucleic acid binding
Homo sapiens ENSG00000239382   alkB, alkylation repair homolog 6 (E. coli)
Leishmania braziliensis LbrM.35.5200   hypothetical protein, conserved
Leishmania donovani LdBPK_365180.1   2OG-Fe(II) oxygenase superfamily, putative
Leishmania infantum LinJ.36.5180   hypothetical protein, conserved
Leishmania major LmjF.36.4950   hypothetical protein, conserved
Leishmania mexicana LmxM.36.4950   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_00731   hypothetical protein
Mus musculus ENSMUSG00000042831   alkB, alkylation repair homolog 6 (E. coli)
Oryza sativa 4348649   Os10g0420000
Onchocerca volvulus OVOC5079  
Schistosoma japonicum Sjp_0090770   Alkylated DNA repair protein alkB homolog 6, putative
Schistosoma japonicum Sjp_0202860   ko:K10768 alkylated DNA repair protein alkB homolog 6, putative
Schistosoma mansoni Smp_120440.1   nucleic acid binding
Schistosoma mansoni Smp_120440.2   nucleic acid binding
Schistosoma mansoni Smp_192130   nucleic acid binding
Schmidtea mediterranea mk4.009172.01   Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
Trypanosoma brucei gambiense Tbg972.11.12280   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.10960   2OG-Fe(II) oxygenase superfamily, putative
Trypanosoma congolense TcIL3000.11.11680   2OG-Fe(II) oxygenase superfamily, putative
Trypanosoma cruzi TcCLB.503971.10   2OG-Fe(II) oxygenase superfamily, putative

Essentiality

Smp_120440.2 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2740 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.2740 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.2740 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.2740 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
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
  • 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
  • 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
  • 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
  • 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.
  • 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
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_120440.2 (Schistosoma mansoni), nucleic acid binding
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