Detailed view for LmjF.30.0130

Basic information

TDR Targets ID: 20874
Leishmania major, lysyl-tRNA synthetase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.6572 | Length (AA): 536 | MW (Da): 60358 | 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

PF00152   tRNA synthetases class II (D, K and N)
PF01336   OB-fold nucleic acid binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004824   lysine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0006430   lysyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Metabolic Pathways

Lysine biosynthesis (KEGG)
Aminoacyl-tRNA biosynthesis (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
1 485 1l0w (A) 31 578 22.00 0 1 0.78 0.55
1 442 1bbu (A) 79 502 40.00 0 1 1.32 -0.55
1 441 4ex5 (A) 80 505 45.00 0 1 1.17996 0.46
2 441 5hgq (B) 72 507 47.00 0 1 1.2311 0.63
2 443 4ycu (A) 140 576 42.00 0 1 1.31653 0.06
4 463 4up8 (A) 70 582 40.00 0 1 1.11611 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
Lower 20-40% 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_147566)

Species Accession Gene Product
Leishmania braziliensis LbrM.30.0140   lysyl-tRNA synthetase, putative
Leishmania donovani LdBPK_300130.1   lysyl-tRNA synthetase, putative
Leishmania infantum LinJ.30.0130   lysyl-tRNA synthetase, putative
Leishmania major LmjF.30.0130   lysyl-tRNA synthetase, putative
Leishmania mexicana LmxM.29.0130   lysyl-tRNA synthetase, putative
Trypanosoma brucei gambiense Tbg972.6.1160   lysyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.6.1510   lysyl-tRNA synthetase, putative
Trypanosoma congolense TcIL3000_6_990   lysyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.503815.20   lysyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.505807.120   lysyl-tRNA synthetase, putative

Essentiality

LmjF.30.0130 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.1510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.1510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.1510 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.1510 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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.30.0130 (Leishmania major), lysyl-tRNA synthetase, putative
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