Detailed view for LmjF.36.5780

Basic information

TDR Targets ID: 29742
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.9622 | Length (AA): 464 | MW (Da): 51026 | 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

PF04189   Gcd10p family

Gene Ontology

Mouse over links to read term descriptions.
GO:0031515   tRNA (m1A) methyltransferase complex  
GO:0003743   translation initiation factor activity  
GO:0030488   tRNA methylation  
GO:0006446   regulation of translational initiation  
GO:0006413   translational initiation  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 4 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
1 413 5eqj (A) 1 451 21.00 0 1 0.766686 1.28
7 411 5ccb (B) 20 460 28.00 0 1 1.08544 0.42
173 264 4l7v (A) 30 137 11.00 0.97 0.02 0.281876 -0.17
407 461 5hmo (A) 804 864 11.00 0.88 0 0.180134 -0.57

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, 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_128776)

Species Accession Gene Product
Arabidopsis thaliana AT2G45730   eukaryotic initiation factor 3 gamma subunit family protein
Babesia bovis BBOV_IV009810   initiation factor 3 gamma subunit containing protein
Brugia malayi Bm1_28855   Eukaryotic initiation factor 3, gamma subunit family protein
Candida albicans CaO19.500   similar to S. cerevisiae GCD10 (YNL062C) tRNA(1-methyladenosine) methyltransferase subunit, translational repressor of GCN4
Candida albicans CaO19.8130   similar to S. cerevisiae GCD10 (YNL062C) tRNA(1-methyladenosine) methyltransferase subunit, translational repressor of GCN4
Caenorhabditis elegans CELE_ZK858.7   Protein ZK858.7
Dictyostelium discoideum DDB_G0281175   tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit
Drosophila melanogaster Dmel_CG9596   CG9596 gene product from transcript CG9596-RC
Echinococcus granulosus EgrG_000106300   tRNA adenine N1 methyltransferase
Entamoeba histolytica EHI_085970   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000106300   tRNA (adenine N(1)) methyltransferase
Homo sapiens ENSG00000089195   tRNA methyltransferase 6
Leishmania braziliensis LbrM.35.6060   hypothetical protein, conserved
Leishmania donovani LdBPK_366030.1   Gcd10p family, putative
Leishmania infantum LinJ.36.6030   hypothetical protein, conserved
Leishmania major LmjF.36.5780   hypothetical protein, conserved
Leishmania mexicana LmxM.36.5780   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_09077   eukaryotic initiation factor 3
Mus musculus ENSMUSG00000037376   tRNA methyltransferase 6
Neospora caninum NCLIV_023490   hypothetical protein, conserved
Oryza sativa 4334938   Os04g0112300
Onchocerca volvulus OVOC8152  
Saccharomyces cerevisiae YNL062C   Gcd10p
Schistosoma japonicum Sjp_0210460   ko:K03256 translation initiation factor eIF-3 subunit P62, putative
Schistosoma japonicum Sjp_0317490   IPR007316,Eukaryotic initiation factor 3, gamma subunit,domain-containing
Schistosoma mansoni Smp_012860   translation initiation factor eif3-related
Schmidtea mediterranea mk4.002395.08   tRNA
Trypanosoma brucei gambiense Tbg972.10.11040   hypothetical protein, conserved
Trypanosoma brucei Tb11.v5.0508   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.9020   Gcd10p family, putative
Trypanosoma congolense TcIL3000_10_7800   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.504171.30   Gcd10p family, putative
Trypanosoma cruzi TcCLB.509795.30   Gcd10p family, putative
Toxoplasma gondii TGME49_281545   eukaryotic initiation factor 3, gamma subunit protein
Theileria parva TP01_0787   hypothetical protein

Essentiality

LmjF.36.5780 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.9020 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.9020 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.9020 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.9020 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK858.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK858.7 Caenorhabditis elegans slow growth wormbase
YNL062C Saccharomyces cerevisiae inviable yeastgenome
TGME49_281545 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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

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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User comments

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Gene identifier LmjF.36.5780 (Leishmania major), hypothetical protein, conserved
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