Detailed view for LmjF.36.5170

Basic information

TDR Targets ID: 22056
Leishmania major, vacuolar protein sorting-associated protein-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.1156 | Length (AA): 209 | MW (Da): 24155 | 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

PF03997   VPS28 protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0032509   endosome transport via multivesicular body sorting pathway  
GO:0000813   ESCRT I complex  

Metabolic Pathways

Endocytosis (KEGG)

Structural information

Modbase 3D models:

There are 6 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
6 94 2f6m (B) 29 118 28.00 0 0.79 0.87 -2.08
106 199 2g3k (A) 148 241 31.00 0 0.84 0.99 -2.56
6 94 2f6m (B) 29 118 28.00 0 0.75 0.867537 -1.22
102 200 2j9w (A) 120 220 32.00 0 0.89 1.04228 -1.87
106 199 2j9u (A) 148 241 34.00 0.0000000091 0.79 0.984861 -1.65
107 163 3k4g (A) 262 321 42.00 0.22 0.53 0.566827 0.6

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_128770)

Species Accession Gene Product
Arabidopsis thaliana AT4G05000   vacuolar protein sorting-associated protein 28-2
Arabidopsis thaliana AT4G21560   vacuolar protein sorting-associated protein 28-1
Babesia bovis BBOV_IV010370   vacuolar sorting protein 28, putative
Brugia malayi Bm1_03915   VPS28 protein homolog
Candida albicans CaO19.212   transport of soluble vacuolar hydrolase precursors
Candida albicans CaO19.7844   transport of soluble vacuolar hydrolase precursors
Dictyostelium discoideum DDB_G0285295   vacuolar protein sorting 28 family protein
Drosophila melanogaster Dmel_CG12770   Vacuolar protein sorting 28
Echinococcus granulosus EgrG_000630700   vacuolar protein sorting associated protein 28
Echinococcus multilocularis EmuJ_000630700   Vacuolar protein sorting associated protein
Homo sapiens ENSG00000160948   vacuolar protein sorting 28 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.35.5420   vacuolar protein sorting-associated protein-like protein
Leishmania donovani LdBPK_365400.1   vacuolar protein sorting-associated protein-like protein
Leishmania infantum LinJ.36.5400   vacuolar protein sorting-associated protein-like protein
Leishmania major LmjF.36.5170   vacuolar protein sorting-associated protein-like protein
Leishmania mexicana LmxM.36.5170   vacuolar protein sorting-associated protein-like protein
Loa Loa (eye worm) LOAG_05532   VPS-28 protein
Mus musculus ENSMUSG00000059323   vacuolar protein sorting 28 (yeast)
Oryza sativa 4327840   Os01g0781000
Saccharomyces cerevisiae YPL065W   ESCRT-I subunit protein VPS28
Schistosoma japonicum Sjp_0211830   Vacuolar protein sorting-associated protein 28 homolog, putative
Schistosoma mansoni Smp_067540   hypothetical protein
Trypanosoma brucei gambiense Tbg972.11.12030   vacuolar sorting-associated protein-like, putative
Trypanosoma brucei Tb927.11.10740   vacuolar sorting-associated protein-like, putative
Trypanosoma congolense TcIL3000.11.11400   vacuolar sorting-associated protein-like, putative
Trypanosoma cruzi TcCLB.506155.50   vacuolar protein sorting-associated protein-like, putative
Theileria parva TP01_0691   hypothetical protein

Essentiality

LmjF.36.5170 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2510 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.2510 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.2510 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.2510 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.36.5170 (Leishmania major), vacuolar protein sorting-associated protein-like protein
Title for this comment
Comment