Detailed view for LmjF.35.2420

Basic information

TDR Targets ID: 27954
Leishmania major, phosphoinositide-binding protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.5075 | Length (AA): 417 | MW (Da): 46559 | Paralog Number: 0

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

PF00787   PX domain
PF09325   Vps5 C terminal like

Gene Ontology

Mouse over links to read term descriptions.
GO:0035091   phosphoinositide binding  
GO:0005515   protein binding  
GO:0007154   cell communication  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
6 139 1h6h (A) 21 140 19.00 0 1 0.29 -0.16
8 137 1xte (A) 9 116 21.00 0.00000000008 0.72 0.42 -0.6
2 173 2csk (A) 6 146 30.00 0.00012 1 0.48677 0.9
8 137 3hpc (X) 30 172 25.00 0 0.8 0.507251 -0.73
162 208 4gqa (A) 175 240 43.00 0.9 0.01 0.31301 0.85
227 371 2p0n (A) 14 154 15.00 0 0.07 0.481222 -0.62

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
Mid 40-60% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 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_128168)

Species Accession Gene Product
Arabidopsis thaliana AT5G06140   sorting nexin 1
Brugia malayi Bm1_35995   PX domain containing protein
Candida albicans CaO19.10385   similar to S. cerevisiae VPS5 (YOR069W) retromer complex protein involved in vacuolar protein sorting
Candida albicans CaO19.2867   similar to S. cerevisiae VPS5 (YOR069W) retromer complex protein involved in vacuolar protein sorting
Caenorhabditis elegans CELE_C05D9.1   Protein SNX-1
Dictyostelium discoideum DDB_G0272989   Phox domain-containing protein
Drosophila melanogaster Dmel_CG2774   Sorting nexin 1
Echinococcus granulosus EgrG_000828200   sorting nexin 2
Echinococcus multilocularis EmuJ_000828200   sorting nexin 2
Homo sapiens 6643   sorting nexin 2
Homo sapiens 6642   sorting nexin 1
Leishmania braziliensis LbrM.34.2370   phosphoinositide-binding protein, putative
Leishmania donovani LdBPK_352470.1   Autophagy-related protein 24
Leishmania infantum LinJ.35.2470   phosphoinositide-binding protein, putative
Leishmania major LmjF.35.2420   phosphoinositide-binding protein, putative
Leishmania mexicana LmxM.34.2420   phosphoinositide-binding protein, putative
Loa Loa (eye worm) LOAG_12649   PX domain-containing protein
Mus musculus ENSMUSG00000034484   sorting nexin 2
Mus musculus ENSMUSG00000032382   sorting nexin 1
Oryza sativa 4324745   Os01g0862300
Saccharomyces cerevisiae YOR069W   Vps5p
Schistosoma japonicum Sjp_0016370   Sorting nexin-2, putative
Schistosoma mansoni Smp_042550   sortingnexin-related
Schmidtea mediterranea mk4.006490.00  
Schmidtea mediterranea mk4.001266.09  
Trypanosoma brucei gambiense Tbg972.9.8370   phosphoinositide-binding protein, putative
Trypanosoma brucei Tb927.9.13380   Autophagy-related protein 24
Trypanosoma cruzi TcCLB.510657.30   Autophagy-related protein 24
Trypanosoma cruzi TcCLB.510749.30   Autophagy-related protein 24

Essentiality

LmjF.35.2420 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4240 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.4240 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.4240 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.4240 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C05D9.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_C05D9.1 Caenorhabditis elegans larval arrest wormbase
CELE_C05D9.1 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • 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.
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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.

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Gene identifier LmjF.35.2420 (Leishmania major), phosphoinositide-binding protein, putative
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