Detailed view for Tb927.9.10350

Basic information

TDR Targets ID: 16771
Trypanosoma brucei, Snf7, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.7289 | Length (AA): 207 | MW (Da): 23469 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF03357   Snf7

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0016192   vesicle-mediated transport  
GO:0015031   protein transport  
GO:0007034   vacuolar transport  

Metabolic Pathways

Endocytosis (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
3 207 5cwm (A) 14 227 17.00 0.044 0.7 1.20284 -0.43
5 170 3frr (A) 7 181 15.00 0 0.81 1.03753 -0.74
7 82 4abm (A) 23 97 20.00 0.12 0.04 0.64865 -1.08
150 205 3eab (G) 148 196 43.00 0.33 0.12 0.217031 0.75

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 Procyclic, Bloodstream Form. 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_127432)

Species Accession Gene Product
Arabidopsis thaliana AT1G17730   ESCRT-related protein CHMP1B
Arabidopsis thaliana AT1G73030   ESCRT-related protein CHMP1A
Babesia bovis BBOV_IV005900   conserved hypothetical protein
Brugia malayi Bm1_25910   RIKEN cDNA 2610002M06
Candida albicans CaO19.11783   class E vacuolar sorting protein
Candida albicans CaO19.4307   class E vacuolar sorting protein
Caenorhabditis elegans CELE_F23C8.6   Protein F23C8.6
Cryptosporidium hominis Chro.10154   hypothetical protein
Cryptosporidium parvum cgd1_1320   developmental protein, putative
Dictyostelium discoideum DDB_G0267394   SNF7 family protein
Drosophila melanogaster Dmel_CG4108   Charged multivesicular body protein 1
Echinococcus granulosus EgrG_000302000   expressed protein
Echinococcus granulosus EgrG_000468500   chmp1 chromatin modifying protein
Echinococcus multilocularis EmuJ_000302000   expressed protein
Echinococcus multilocularis EmuJ_000468500   chmp1 (chromatin modifying protein)
Giardia lamblia GL50803_15472   Hypothetical protein
Giardia lamblia GL50803_24947   Hypothetical protein
Homo sapiens ENSG00000255112   charged multivesicular body protein 1B
Leishmania braziliensis LbrM.34.4380   hypothetical protein, conserved
Leishmania donovani LdBPK_354470.1   Snf7, putative
Leishmania infantum LinJ.35.4470   hypothetical protein, conserved
Leishmania major LmjF.35.4400   hypothetical protein, conserved
Leishmania mexicana LmxM.34.4400   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_08338   hypothetical protein
Mus musculus 67064   charged multivesicular body protein 1B
Mus musculus 102642050   charged multivesicular body protein 1a-like
Mus musculus ENSMUSG00000000743   charged multivesicular body protein 1A
Mus musculus ENSMUSG00000031242   RIKEN cDNA 2610002M06 gene
Oryza sativa 4341638   Os06g0643300
Plasmodium berghei PBANKA_0415200   vacuolar protein sorting-associated protein 46, putative
Plasmodium falciparum PF3D7_0906100   vacuolar protein sorting-associated protein 46, putative
Plasmodium knowlesi PKNH_0703900   vacuolar protein sorting-associated protein 46, putative
Plasmodium vivax PVX_098750   vacuolar protein sorting-associated protein 46, putative
Plasmodium yoelii PY07558   developmental protein DG1118
Saccharomyces cerevisiae YKR035W-A   Did2p
Schistosoma japonicum Sjp_0071040   Charged multivesicular body protein 1a, putative
Schistosoma japonicum Sjp_0205770   Charged multivesicular body protein 1b, putative
Schistosoma japonicum Sjp_0308980   expressed protein
Schistosoma mansoni Smp_079000   vacuolar assembly/sorting protein D1D2-like protein
Schistosoma mansoni Smp_055880.1   chmp1 (chromatin modifying protein) (charged multivesicular body protein)
Schistosoma mansoni Smp_055880.2   chmp1 (chromatin modifying protein) (charged multivesicular body protein)
Schmidtea mediterranea mk4.004926.01   Charged multivesicular body protein 1a
Schmidtea mediterranea mk4.004926.00   Charged multivesicular body protein 1a
Schmidtea mediterranea mk4.000599.01   Charged multivesicular body protein 1b
Trypanosoma brucei gambiense Tbg972.9.6010   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.10350   Snf7, putative
Trypanosoma congolense TcIL3000_9_3920   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.506147.220   Snf7, putative
Trypanosoma cruzi TcCLB.510733.20   Snf7, putative
Toxoplasma gondii TGME49_315350   SNF7 family protein
Theileria parva TP01_0395   hypothetical protein, conserved
Trichomonas vaginalis TVAG_247500   Charged multivesicular body protein 1B, putative
Trichomonas vaginalis TVAG_011650   Charged multivesicular body protein 1B, putative
Trichomonas vaginalis TVAG_151500   chmp1, putative

Essentiality

Tb927.9.10350 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.1770 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.1770 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.1770 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.1770 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F23C8.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_F23C8.6 Caenorhabditis elegans larval arrest wormbase
CELE_F23C8.6 Caenorhabditis elegans larval lethal wormbase
CELE_F23C8.6 Caenorhabditis elegans slow growth wormbase
TGME49_315350 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • 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
  • 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.

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 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 Tb927.9.10350 (Trypanosoma brucei), Snf7, putative
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