Detailed view for LmjF.03.0060

Basic information

TDR Targets ID: 25635
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.8343 | Length (AA): 390 | MW (Da): 43222 | Paralog Number: 0

Signal peptide: Y | 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

PF02475   Met-10+ like-protein

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
107 389 2frn (A) 19 275 30.00 0 1 0.83 -0.11
135 388 2frn (A) 26 274 30.00 0 1 1.02 -0.53
190 387 2frn (A) 86 273 41.00 0 1 1.02 -0.94
59 389 3k6r (A) 6 275 32.00 0 1 0.935718 0.53
180 390 3a27 (A) 37 247 35.00 0 1 0.976026 -0.35
192 390 3a27 (A) 59 247 41.00 0 1 0.980656 -0.45
230 323 3eey (G) 21 128 16.00 0 0.31 0.424426 -0.61

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 60-80% 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_129346)

Species Accession Gene Product
Arabidopsis thaliana AT4G04670   Met-10+ like family protein / kelch repeat-containing protein
Brugia malayi Bm1_51625   Met-10+ like-protein
Candida albicans CaO19.7369   similar to S. cerevisiae YML005W
Caenorhabditis elegans CELE_F40F9.10   Protein F40F9.10
Homo sapiens ENSG00000183665   tRNA methyltransferase 12 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.03.0070   hypothetical protein, conserved
Leishmania donovani LdBPK_030050.1   Met-10+ like-protein, putative
Leishmania infantum LinJ.03.0050   hypothetical protein, conserved
Leishmania major LmjF.03.0060   hypothetical protein, conserved
Leishmania mexicana LmxM.03.0060   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_02567   hypothetical protein
Loa Loa (eye worm) LOAG_14175   hypothetical protein
Mus musculus ENSMUSG00000037085   tRNA methyltranferase 12
Oryza sativa 4343372   Os07g0515000
Plasmodium berghei PBANKA_0502800   tRNA wybutosine-synthesizing protein, putative
Plasmodium falciparum PF3D7_1018600   tRNA wybutosine-synthesizing protein, putative
Plasmodium knowlesi PKNH_0602900   tRNA wybutosine-synthesizing protein, putative
Plasmodium yoelii PY05008   Unknown protein
Saccharomyces cerevisiae YML005W   Trm12p
Trypanosoma brucei gambiense Tbg972.10.3900   hypothetical protein, conserved,predicted to be involved in methionine biosynthesis
Trypanosoma brucei Tb927.10.3080   methionine biosynthetic protein, putative
Trypanosoma congolense TcIL3000_10_2530   predicted to be involved in methionine biosynthesis
Trypanosoma cruzi TcCLB.510943.180   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.504867.110   hypothetical protein, conserved
Toxoplasma gondii TGME49_234490   kelch repeat-containing protein
Theileria parva TP02_0179   hypothetical protein

Essentiality

LmjF.03.0060 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3080 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.3080 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.3080 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.3080 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0502800 Plasmodium berghei Essential plasmo
TGME49_234490 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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
  • 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.
  • 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.

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.03.0060 (Leishmania major), hypothetical protein, conserved
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