Detailed view for LmjF.21.0910

Basic information

TDR Targets ID: 24352
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.6643 | Length (AA): 275 | MW (Da): 29852 | 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

PF04073   Aminoacyl-tRNA editing domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0002161   GO:aminoacyl-tRNA editing activity  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
83 263 2cx5 (A) 4 157 19.00 0 1 0.74 -0.74
91 264 1dbu (A) 6 158 16.00 0 0.71 0.66 -0.81
120 261 1dbu (A) 35 155 21.00 0 0.6 0.647964 -0.48
120 262 2dxa (A) 23 156 20.00 0 0.97 0.7426 -0.4
189 262 1wdv (A) 80 151 32.00 0.032 0.83 0.633991 0.11

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_133573)

Species Accession Gene Product
Arabidopsis thaliana AT4G16510   YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
Dictyostelium discoideum DDB_G0268796   hypothetical protein
Entamoeba histolytica EHI_044760   Rho guanine nucleotide exchange factor, putative
Giardia lamblia GL50803_14486   hypothetical protein
Leishmania braziliensis LbrM.32.1250   hypothetical protein, conserved
Leishmania donovani LdBPK_211150.1   Aminoacyl-tRNA editing domain containing protein, putative
Leishmania infantum LinJ.21.1150   hypothetical protein, conserved
Leishmania major LmjF.21.0910   hypothetical protein, conserved
Leishmania mexicana LmxM.21.0910   hypothetical protein, conserved
Neospora caninum NCLIV_029240   YbaK / prolyl-tRNA synthetases associated domain containing protein, putative
Oryza sativa 4330228   Os02g0662200
Trypanosoma brucei gambiense Tbg972.10.1450   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.1250   Aminoacyl-tRNA editing domain containing protein, putative
Trypanosoma cruzi TcCLB.509967.40   Aminoacyl-tRNA editing domain containing protein, putative
Trypanosoma cruzi TcCLB.509695.20   Aminoacyl-tRNA editing domain containing protein, putative
Toxoplasma gondii TGME49_255680   YbaK/proline-tRNA ligase associated domain-containing protein
Trichomonas vaginalis TVAG_140400   conserved hypothetical protein

Essentiality

LmjF.21.0910 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.1250 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.1250 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.1250 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.1250 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_255680 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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.21.0910 (Leishmania major), hypothetical protein, conserved
Title for this comment
Comment