Detailed view for LmjF.35.0580

Basic information

TDR Targets ID: 23385
Leishmania major, SNF-7-like protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.4966 | Length (AA): 224 | MW (Da): 25562 | 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

PF03357   Snf7

Gene Ontology

Mouse over links to read term descriptions.
GO:0007034   vacuolar transport  
GO:0015031   protein transport  

Metabolic Pathways

Endocytosis (KEGG)

Structural information

Modbase 3D models:

There are 5 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
12 148 2gd5 (A) 12 164 15.00 0 0.09 0.74 -0.12
9 188 4uos (A) 2 177 11.00 0.6 0.04 0.960471 -0.93
10 220 4cgk (A) 45 251 13.00 0.32 0.01 1.00286 0.2
33 145 2qih (A) 534 645 9.00 0 0 0.555064 -0.09
149 189 4txr (C) 151 190 43.00 0.053 0.11 0.538536 0.57

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 amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_128328)

Species Accession Gene Product
Arabidopsis thaliana AT3G10640   vacuolar protein sorting protein 60.1
Arabidopsis thaliana AT5G04850   vacuolar protein sorting protein 60.2
Brugia malayi Bm1_52890   MGC80100 protein
Candida albicans CaO19.3401   similar to S. cerevisiae VPS60 (YDR486C) involved in vacuolar protein sorting
Candida albicans CaO19.10904   similar to S. cerevisiae VPS60 (YDR486C) involved in vacuolar protein sorting
Caenorhabditis elegans CELE_F41E6.9   Protein F41E6.9
Dictyostelium discoideum DDB_G0287993   SNF7 family protein
Drosophila melanogaster Dmel_CG6259   CG6259 gene product from transcript CG6259-RB
Echinococcus granulosus EgrG_001063800   charged multivesicular body protein 5
Entamoeba histolytica EHI_114790   SNF7 family protein
Echinococcus multilocularis EmuJ_001063800   charged multivesicular body protein 5
Homo sapiens ENSG00000086065   charged multivesicular body protein 5
Leishmania braziliensis LbrM.34.0580   SNF-7-like protein, conserved
Leishmania donovani LdBPK_350580.1   SNF-7-like protein, conserved
Leishmania infantum LinJ.35.0580   SNF-7-like protein, conserved
Leishmania major LmjF.35.0580   SNF-7-like protein, conserved
Leishmania mexicana LmxM.34.0580   SNF-7-like protein, conserved
Loa Loa (eye worm) LOAG_11989   hypothetical protein
Mus musculus ENSMUSG00000028419   charged multivesicular body protein 5
Oryza sativa 4337536   Os05g0102900
Oryza sativa 9266052   Os01g0102950
Plasmodium berghei PBANKA_1305700   vacuolar-sorting protein SNF7, putative
Plasmodium falciparum PF3D7_1441800   vacuolar-sorting protein SNF7, putative
Plasmodium knowlesi PKNH_1240500   vacuolar-sorting protein SNF7, putative
Plasmodium vivax PVX_118400   vacuolar-sorting protein SNF7, putative
Plasmodium yoelii PY01293   CTA1p, putative
Saccharomyces cerevisiae YDR486C   Vps60p
Schistosoma japonicum Sjp_0076120   Charged multivesicular body protein 5, putative
Schistosoma mansoni Smp_010090   snf7-related
Schmidtea mediterranea mk4.012846.01   Charged multivesicular body protein 5
Schmidtea mediterranea mk4.002224.04   Charged multivesicular body protein 5
Trypanosoma brucei gambiense Tbg972.10.4790   SNF-7-like protein, putative
Trypanosoma brucei Tb927.10.3860   SNF-7-like protein, putative
Trypanosoma congolense TcIL3000_10_3200   SNF-7-like protein, putative
Trypanosoma cruzi TcCLB.511001.100   SNF-7-like protein, putative
Trypanosoma cruzi TcCLB.506957.110   SNF-7-like protein, putative
Trichomonas vaginalis TVAG_123830   Charged multivesicular body protein, putative
Trichomonas vaginalis TVAG_396070   Charged multivesicular body protein, putative

Essentiality

LmjF.35.0580 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3860 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.3860 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.3860 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.10.3860 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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

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 LmjF.35.0580 (Leishmania major), SNF-7-like protein, conserved
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