Detailed view for LmjF.36.6350

Basic information

TDR Targets ID: 21597
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.2349 | Length (AA): 510 | MW (Da): 58035 | 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

PF04857   CAF1 family ribonuclease

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0003676   nucleic acid 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
1 380 2a1s (A) 1 401 25.00 0 1 1.05 -0.66
140 219 1ug8 (A) 5 82 14.00 0.000000043 0.69 0.43 -0.98
1 379 2a1s (A) 1 400 26.00 0 1 0.955837 0.21
1 491 3d45 (B) 1 502 23.00 0 1 0.692145 1.69
342 455 4o1g (A) 85 190 32.00 0.69 0.03 0.154229 1.66

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_128150)

Species Accession Gene Product
Arabidopsis thaliana AT1G55870   poly(A)-specific ribonuclease PARN
Babesia bovis BBOV_II007020   CAF1 family ribonuclease containing protein
Caenorhabditis elegans CELE_K10C8.1   Protein K10C8.1
Homo sapiens ENSG00000140694   poly(A)-specific ribonuclease
Homo sapiens ENSG00000146453   poly(A)-specific ribonuclease (PARN)-like domain containing 1
Leishmania braziliensis LbrM.23.0650   hypothetical protein, conserved
Leishmania donovani LdBPK_230660.1   hypothetical protein, conserved
Leishmania donovani LdBPK_366630.1   poly(A)-specific ribonuclease PARN, putative
Leishmania infantum LinJ.36.6630   hypothetical protein, conserved
Leishmania infantum LinJ.23.0660   hypothetical protein, conserved
Leishmania major LmjF.36.6350   hypothetical protein, conserved
Leishmania major LmjF.23.1630   hypothetical protein, conserved
Leishmania mexicana LmxM.23.1630   hypothetical protein, conserved
Leishmania mexicana LmxM.36.6350   hypothetical protein, conserved
Mus musculus ENSMUSG00000022685   poly(A)-specific ribonuclease (deadenylation nuclease)
Mus musculus ENSMUSG00000073460   poly(A)-specific ribonuclease (PARN)-like domain containing 1
Neospora caninum NCLIV_033510   hypothetical protein
Oryza sativa 9268289   Os04g0467400
Plasmodium berghei PBANKA_1307400   poly(A)-specific ribonuclease PARN, putative
Plasmodium falciparum PF3D7_1443500   poly(A)-specific ribonuclease PARN, putative
Plasmodium knowlesi PKNH_1238800   poly(A)-specific ribonuclease PARN, putative
Plasmodium vivax PVX_118315   poly(A)-specific ribonuclease PARN, putative
Plasmodium yoelii PY01911   hypothetical protein
Schmidtea mediterranea mk4.001575.02  
Schmidtea mediterranea mk4.000807.10  
Trypanosoma brucei gambiense Tbg972.10.10190   ribonuclease, putative
Trypanosoma brucei gambiense Tbg972.8.2440   ribonuclease, putative
Trypanosoma brucei Tb927.10.8360   Poly(A)-specific ribonuclease PARN-2
Trypanosoma brucei Tb927.8.2850   Poly(A)-specific ribonuclease PARN-1
Trypanosoma congolense TcIL3000_0_41370   Poly(A)-specific ribonuclease PARN-1
Trypanosoma congolense TcIL3000_10_7200   ribonuclease, putative
Trypanosoma cruzi TcCLB.508231.74   poly(A)-specific ribonuclease PARN, putative
Trypanosoma cruzi TcCLB.506251.100   poly(A)-specific ribonuclease PARN, putative
Trypanosoma cruzi TcCLB.507221.20   poly(A)-specific ribonuclease PARN, putative
Trypanosoma cruzi TcCLB.504427.200   poly(A)-specific ribonuclease PARN, putative
Theileria parva TP02_0676   hypothetical protein, conserved

Essentiality

LmjF.36.6350 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.2850 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.2850 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.2850 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.8.2850 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.10.8360 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.8360 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.8360 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.8360 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_1307400 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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.36.6350 (Leishmania major), hypothetical protein, conserved
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