Detailed view for Tb927.2.5120

Basic information

TDR Targets ID: 55216
Trypanosoma brucei, Vesicle-associated membrane protein 7
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.1899 | Length (AA): 221 | MW (Da): 25314 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 1

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

PF00957   Synaptobrevin
PF13774   Regulated-SNARE-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0006944   membrane fusion  
GO:0003674   molecular_function  
GO:0016021   integral to membrane  
GO:0005886   plasma membrane  
GO:0016192   vesicle-mediated transport  
GO:0006810   transport  

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
1 167 4b93 (A) 1 163 29.00 0 1 1.16396 -1.06
2 127 2nut (C) 1 149 10.00 0.000000025 0.53 0.742436 -1.17
4 183 3kyq (A) 25 192 24.00 0.000000000082 1 1.08978 -0.13
67 135 2d4c (A) 40 119 32.00 0.17 0.04 0.487217 0.51

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

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Procyclic. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_127735)

Species Accession Gene Product
Arabidopsis thaliana AT4G32150   vesicle-associated membrane protein 711
Arabidopsis thaliana AT1G04760   vesicle-associated membrane protein 726
Arabidopsis thaliana AT2G32670   vesicle-associated membrane protein 725
Arabidopsis thaliana AT5G22360   vesicle-associated membrane protein 714
Arabidopsis thaliana AT2G33120   vesicle-associated membrane protein 722
Arabidopsis thaliana AT2G25340   vesicle-associated membrane protein 712
Arabidopsis thaliana AT5G11150   vesicle-associated membrane protein 713
Brugia malayi Bm1_39365   Synaptobrevin family protein
Cryptosporidium hominis Chro.60028   synaptobrevin-like protein
Cryptosporidium parvum cgd6_170   synaptobrevin-like protein, possible
Dictyostelium discoideum DDB_G0277173   longin domain-containing protein
Drosophila melanogaster Dmel_CG1599   Vesicle-associated membrane protein 7
Entamoeba histolytica EHI_170040   longin-type vesicle-associated membrane protein, putative
Homo sapiens ENSG00000124333   vesicle-associated membrane protein 7
Leishmania braziliensis LbrM.27.2560   vesicle-associated membrane protein (vamp), putative
Leishmania donovani LdBPK_272300.1   Vesicle-associated membrane protein 7
Leishmania infantum LinJ.27.2300   vesicle-associated membrane protein (vamp), putative
Leishmania major LmjF.27.2350   R-SNARE protein, putative
Leishmania mexicana LmxM.27.2350   vesicle-associated membrane protein (vamp), putative
Loa Loa (eye worm) LOAG_13749   synaptobrevin family protein
Mus musculus 102639650   predicted gene, 35911
Mus musculus ENSMUSG00000051412   vesicle-associated membrane protein 7
Neospora caninum NCLIV_030950   hypothetical protein
Oryza sativa 4331049   Os02g0803600
Oryza sativa 4342638   Os07g0194000
Oryza sativa 4348130   Os10g0154000
Oryza sativa 4340278   Os06g0174400
Oryza sativa 4334472   Os03g0803000
Plasmodium berghei PBANKA_1401700   SNARE protein, putative
Plasmodium falciparum PF3D7_1303200   SNARE protein, putative
Plasmodium knowlesi PKNH_1403400   SNARE protein, putative
Plasmodium vivax PVX_122000   SNARE protein, putative
Plasmodium yoelii PY03903   Arabidopsis thaliana At5g22360/MWD9_16, putative
Schmidtea mediterranea mk4.002453.01   Vesicle-associated membrane protein 7
Trypanosoma brucei gambiense Tbg.972.2.3150   vesicle-associated membrane protein, putative,synaptobrevin, putative
Trypanosoma brucei Tb927.2.5120   Vesicle-associated membrane protein 7
Trypanosoma congolense TcIL3000_5_3990   vesicle-associated membrane protein, putative
Trypanosoma cruzi TcCLB.507801.179   Vesicle-associated membrane protein 7
Trypanosoma cruzi TcCLB.511627.60   Vesicle-associated membrane protein 7
Toxoplasma gondii TGME49_230430   vesicle-associated membrane protein, putative
Trichomonas vaginalis TVAG_476920   snb-1, putative
Trichomonas vaginalis TVAG_037100   vAMP-4, putative
Trichomonas vaginalis TVAG_477050   vAMP-7, putative
Trichomonas vaginalis TVAG_249080   snare proteins, putative
Trichomonas vaginalis TVAG_449870   snare proteins, putative

Essentiality

Tb927.2.5120 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.5120 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.2.5120 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.2.5120 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.2.5120 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_1401700 Plasmodium berghei Dispensable plasmo
TGME49_230430 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

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Gene identifier Tb927.2.5120 (Trypanosoma brucei), Vesicle-associated membrane protein 7
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