Detailed view for LmjF.16.1130

Basic information

TDR Targets ID: 26591
Leishmania major, tyrosyl or methionyl-tRNA synthetase-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.1229 | Length (AA): 180 | MW (Da): 19655 | Paralog Number: 1

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

PF01588   Putative tRNA binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0000049   tRNA binding  

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
2 180 1ntg (A) 8 170 41.00 0 1 1.41 -0.28
2 121 2cwp (A) 13 112 32.00 0 1 0.78 -0.3
2 180 1ntg (A) 8 170 44.00 0 1 1.42874 -0.53
8 84 1gd7 (A) 14 84 34.00 0.22 0.58 0.733078 -0.26
8 120 1mkh (A) 15 106 49.00 0 1 0.985378 -0.33

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_127125)

Species Accession Gene Product
Arabidopsis thaliana AT3G59980   Nucleic acid-binding, OB-fold-like protein
Arabidopsis thaliana AT2G40660   nucleic acid-binding, OB-fold-like protein
Babesia bovis BBOV_III010240   tRNA binding domain containing protein
Candida albicans CaO19.10141   one of two distinct genes similar to S. cerevisiae ARC1 (YGL105W) component of amino acyl-tRNA synthetase complexes
Candida albicans CaO19.9960   one of two distinct genes similar to S. cerevisiae ARC1 (YGL105W) tRNA-binding component of amino acyl-tRNA synthetase complexes
Candida albicans CaO19.2610   one of two distinct genes similar to S. cerevisiae ARC1 (YGL105W) component of amino acyl-tRNA synthetase complexes
Candida albicans CaO19.2422   one of two distinct genes similar to S. cerevisiae ARC1 (YGL105W) tRNA-binding component of amino acyl-tRNA synthetase complexes
Cryptosporidium hominis Chro.40444   similar to tyrosyl-tRNA synthetase
Cryptosporidium parvum cgd4_3880   emap RNA binding domain protein (N terminal low complexity region)
Dictyostelium discoideum DDB_G0291926   endothelial monocyte-activating polypeptide II precursor pro-EMAP II family protein
Dictyostelium discoideum DDB_G0275611   hypothetical protein
Drosophila melanogaster Dmel_CG8235   CG8235 gene product from transcript CG8235-RA
Escherichia coli b3074   putative tRNA binding protein
Echinococcus granulosus EgrG_001100200   aminoacyl tRNA synthase complex interacting
Echinococcus multilocularis EmuJ_001100200   aminoacyl tRNA synthase complex interacting
Giardia lamblia GL50803_4606   Methionyl-tRNA synthetase
Homo sapiens ENSG00000164022   aminoacyl tRNA synthetase complex-interacting multifunctional protein 1
Leishmania braziliensis LbrM.16.1160   tyrosyl or methionyl-tRNA synthetase-like protein
Leishmania braziliensis LbrM.22.0420   hypothetical protein, conserved
Leishmania donovani LdBPK_161170.1   tyrosyl or methionyl-tRNA synthetase-like protein
Leishmania donovani LdBPK_220350.1   Putative tRNA binding domain containing protein, putative
Leishmania infantum LinJ.16.1170   tyrosyl or methionyl-tRNA synthetase-like protein
Leishmania infantum LinJ.22.0350   hypothetical protein, conserved
Leishmania major LmjF.22.0470   hypothetical protein, conserved
Leishmania major LmjF.16.1130   tyrosyl or methionyl-tRNA synthetase-like protein
Leishmania mexicana LmxM.16.1130   tyrosyl or methionyl-tRNA synthetase-like protein
Leishmania mexicana LmxM.22.0470   hypothetical protein, conserved
Mus musculus ENSMUSG00000028029   aminoacyl tRNA synthetase complex-interacting multifunctional protein 1
Neospora caninum NCLIV_006150   tRNA binding domain containing protein, related
Oryza sativa 4335424   Os04g0303900
Oryza sativa 4327613   Os01g0821800
Plasmodium berghei PBANKA_1306200   tRNA import protein tRIP, putative
Plasmodium falciparum PF3D7_1442300   tRNA import protein tRIP
Plasmodium knowlesi PKNH_1240000   tRNA import protein tRIP, putative
Plasmodium vivax PVX_118375   methionine-tRNA ligase, putative
Plasmodium yoelii PY02994   putative methionyl-tRNA synthetase
Saccharomyces cerevisiae YGL105W   Arc1p
Schistosoma japonicum Sjp_0303990   Methionyl-tRNA synthetase, cytoplasmic, putative
Schistosoma mansoni Smp_073620   methionyl-tRNA synthetase
Schmidtea mediterranea mk4.007045.03   Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Schmidtea mediterranea mk4.017740.00   Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Trypanosoma brucei gambiense Tbg972.8.5270   tyrosyl/methionyl-tRNA synthetase, putative
Trypanosoma brucei gambiense Tbg972.7.2670   tyrosyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.8.5330   tyrosyl/methionyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.7.2400   tyrosyl-tRNA synthetase, putative
Trypanosoma congolense TcIL3000_8_5170   tyrosyl/methionyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.511217.200   tyrosyl or methionyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.506573.30   tyrosyl or methionyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.509207.50   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.508321.50   hypothetical protein, conserved
Toxoplasma gondii TGME49_223140   tRNA binding domain-containing protein
Theileria parva TP02_0124   methionyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_336920   conserved hypothetical protein
Trichomonas vaginalis TVAG_043270   conserved hypothetical protein
Trichomonas vaginalis TVAG_328570   conserved hypothetical protein
Trichomonas vaginalis TVAG_000070   methionyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_228330   conserved hypothetical protein

Essentiality

LmjF.16.1130 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.5330 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.5330 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.5330 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.8.5330 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.7.2400 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.2400 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.2400 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.2400 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3074 Escherichia coli non-essential goodall
PBANKA_1306200 Plasmodium berghei Slow plasmo
TGME49_223140 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

Druggability index (range: 0 to 1): 0.2

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0094 0.4118 0
0.0093 0.2505 0.5972
0.0078 0.4068 0

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

3 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier LmjF.16.1130 (Leishmania major), tyrosyl or methionyl-tRNA synthetase-like protein
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