Detailed view for Smp_034210

Basic information

TDR Targets ID: 283876
Schistosoma mansoni, vam6/vps39 related
Source Database / ID:  GeneDB

pI: 8.2378 | Length (AA): 1211 | MW (Da): 138337 | Paralog Number: 3

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

PF00780   CNH domain
PF10366   Vacuolar sorting protein 39 domain 1
PF10367   Vacuolar sorting protein 39 domain 2

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0005488   binding  
GO:0016192   vesicle-mediated transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
336 1175 2x19 (B) 33 865 12.00 0 1 0.716842 0.37

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_128864)

Species Accession Gene Product
Arabidopsis thaliana AT4G36630   protein EMBRYO DEFECTIVE 2754
Brugia malayi Bm1_00995   hypothetical protein
Candida albicans CaO19.1568   similar to C terminus of S. cerevisiae Rab guanyl-nucleotide exchange factor VAM6 (YDL077C) involved in vacuolar morphogenesis
Candida albicans CaO19.9141   similar to C terminus of S. cerevisiae Rab guanyl-nucleotide exchange factor VAM6 (YDL077C) involved in vacuolar morphogenesis
Candida albicans CaO19.1567   similar to N terminus of S. pombe VAM6-like putative vacuolar protein vps39 (SPAC23H4.14)
Candida albicans CaO19.9140   similar to N terminus of S. pombe VAM6-like putative vacuolar protein vps39 (SPAC23H4.14)
Caenorhabditis elegans CELE_T08G5.5   Protein VPS-39, isoform C
Dictyostelium discoideum DDB_G0279169   citron-like domain-containing protein
Drosophila melanogaster Dmel_CG7146   Vacuolar protein sorting 39
Echinococcus granulosus EgrG_001200800   Vam6:Vps39 protein
Echinococcus multilocularis EmuJ_001200800   Vam6:Vps39 protein
Homo sapiens ENSG00000166887   vacuolar protein sorting 39 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.20.6010   hypothetical protein, conserved
Leishmania donovani LdBPK_120910.1   Vacuolar sorting protein 39 domain 1/Vacuolar sorting protein 39 domain 2, putative
Leishmania infantum LinJ.12.0910   hypothetical protein, conserved
Leishmania major LmjF.12.1320   hypothetical protein, conserved
Leishmania mexicana LmxM.12.1320   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_10497   hypothetical protein
Loa Loa (eye worm) LOAG_11035   hypothetical protein
Mus musculus ENSMUSG00000027291   vacuolar protein sorting 39 (yeast)
Oryza sativa 4333909   Os03g0715500
Saccharomyces cerevisiae YDL077C   Vam6p
Schistosoma japonicum Sjp_0209840   expressed protein
Schistosoma japonicum Sjp_0116730   hypothetical protein
Schistosoma mansoni Smp_193210   hypothetical protein
Schistosoma mansoni Smp_192990   hypothetical protein
Schistosoma mansoni Smp_188660   hypothetical protein
Schistosoma mansoni Smp_034210   vam6/vps39 related
Schmidtea mediterranea mk4.010238.00  
Schmidtea mediterranea mk4.015131.01  
Trypanosoma brucei gambiense Tbg972.1.3280   hypothetical protein, conserved
Trypanosoma brucei Tb927.1.4760   Vacuolar sorting protein 39 domain 1/Vacuolar sorting protein 39 domain 2, putative
Trypanosoma congolense TcIL3000_1_1970   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.507997.60   Vacuolar sorting protein 39 domain 1/Vacuolar sorting protein 39 domain 2, putative
Trypanosoma cruzi TcCLB.508593.50   Vacuolar sorting protein 39 domain 1/Vacuolar sorting protein 39 domain 2, putative
Trypanosoma cruzi TcCLB.508823.90   hypothetical protein
Trichomonas vaginalis TVAG_027270   conserved hypothetical protein

Essentiality

Smp_034210 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.1.4760 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.1.4760 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.1.4760 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.1.4760 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T08G5.5 Caenorhabditis elegans embryonic lethal wormbase
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.021 0.2843 0.2843
0.0106 0.2606 0.2606
0.1143 0.2896 0.2896
0.1353 0.2901 0.2901
0.1197 0.2898 0.2898
0.1686 0.291 0.291
0.0904 0.2886 0.2885
0.168 0.2909 0.2909
0.1048 0.2891 0.2891
0.1466 0.2905 0.2905
0.103 0.292 0.2916
0.0106 0.2801 0.2801
0.0434 0.2896 0.2892
0.1186 0.2896 0.2896
0.1087 0.2894 0.2894
0.0105 0.2743 0.2743
0.1099 0.2894 0.2894
0.1613 0.2909 0.2908
0.1433 0.2847 0.2845
0.103 0.292 0.2916
0.0106 0.2606 0.2606
0.1682 0.2913 0.2913
0.0187 0.2552 0.2552
0.1099 0.2894 0.2894
0.1073 0.2894 0.2894
0.1459 0.2906 0.2906
0.1623 0.2923 0.2921
0.1303 0.2902 0.2902
0.0802 0.2898 0.2829
0.1237 0.2904 0.2904
0.1087 0.2894 0.2894
0.0132 0.2746 0.2746
0.1172 0.2919 0.2915
0.0569 0.2893 0.2893
0.0633 0.2895 0.2867
0.0181 0.253 0.253
0.1433 0.2847 0.2845
0.1353 0.2902 0.2902
0.1087 0.2894 0.2894
0.1171 0.2874 0.2856
0.1087 0.2894 0.2894
0.0929 0.2913 0.2913
0.1682 0.2913 0.2913
0.0408 0.287 0.287
0.1433 0.2847 0.2845
0.1682 0.2913 0.2913
0.0408 0.287 0.287
0.0926 0.2605 0.2596
0.1385 0.2902 0.2902
0.1433 0.2847 0.2845
0.1433 0.2847 0.2845
0.0508 0.2884 0.2884
0.0982 0.2914 0.2914
0.0106 0.2606 0.2606
0.0125 0.2749 0.2749
0.1304 0.2902 0.2902
0.1105 0.2892 0.2892
0.0233 0.2817 0.2702
0.1086 0.2895 0.2895
0.0286 0.2813 0.276
0.1034 0.2918 0.2918
0.021 0.2843 0.2843
0.0132 0.2746 0.2746
0.0187 0.2552 0.2552
0.1007 0.2883 0.2883
0.0986 0.2789 0.2789
0.0383 0.2634 0.2634
0.1149 0.2895 0.2894
0.0132 0.2746 0.2746
0.1024 0.2852 0.2852
0.0105 0.2609 0.2609
0.1433 0.2847 0.2845
0.0187 0.2552 0.2552
0.1252 0.2903 0.2903
0.0152 0.2829 0.2816
0.0884 0.2885 0.2885
0.1433 0.2847 0.2845
0.1083 0.2894 0.2894
0.0904 0.2911 0.2911
0.1019 0.2786 0.2786
0.1195 0.2898 0.2898
0.0157 0.2799 0.2799
0.0359 0.286 0.286
0.0186 0.274 0.274
0.1385 0.2902 0.2902
0.0406 0.2899 0.287
0.1433 0.2847 0.2845
0.1132 0.2894 0.2894
0.1165 0.2901 0.2901
0.0333 0.2853 0.2853
0.1158 0.2901 0.2901
0.0127 0.2567 0.2567
0.1433 0.2847 0.2845
0.1077 0.2892 0.2892
0.0152 0.2829 0.2816
0.1433 0.2847 0.2845
0.0997 0.2898 0.2898
0.0807 0.2881 0.2881
0.1433 0.2847 0.2845
0.0802 0.2898 0.2829
0.055 0.289 0.289
0.1312 0.2901 0.2901
0.0437 0.2896 0.2892
0.1682 0.2913 0.2913
0.1229 0.29 0.29
0.1559 0.2906 0.2906
0.1623 0.2923 0.2921
0.1433 0.2847 0.2845
0.1183 0.2897 0.2897
0.1433 0.2847 0.2845
0.1433 0.2847 0.2845
0.1528 0.2907 0.2907

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.

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User comments

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Gene identifier Smp_034210 (Schistosoma mansoni), vam6/vps39 related
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