Detailed view for LmjF.36.4895

Basic information

TDR Targets ID: 24253
Leishmania major, exosome-associated protein 4, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.0378 | Length (AA): 221 | MW (Da): 23389 | 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

PF01138   3' exoribonuclease family, domain 1

Gene Ontology

Mouse over links to read term descriptions.
GO:0003723   RNA binding  
GO:0000175   3'-5'-exoribonuclease activity  
GO:0006396   RNA processing  

Metabolic Pathways

RNA degradation (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
2 221 2br2 (B) 18 241 24.00 0 1 1.32 -0.64
1 220 1r6l (A) 1 237 20.00 0 1 1.15708 0.05
2 221 2br2 (B) 18 241 25.00 0 1 1.30008 0.09
6 215 2nn6 (F) 29 257 33.00 0 1 1.22163 0.69
20 145 5jea (F) 50 196 25.00 0.0084 1 0.820536 -0.2

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_128529)

Species Accession Gene Product
Arabidopsis thaliana AT4G27490   3'-5'-exoribonuclease family protein
Babesia bovis BBOV_III011810   conserved hypothetical protein
Brugia malayi Bm1_24220   3' exoribonuclease family, domain 1 containing protein
Candida albicans CaO19.7801   similar to S. cerevisiae MTR3 (YGR158C) exosome component involved mRNA degradation and nuclear RNA processing
Candida albicans CaO19.168   similar to S. cerevisiae MTR3 (YGR158C) exosome component involved mRNA degradation and nuclear RNA processing
Caenorhabditis elegans CELE_Y6D11A.1   Protein EXOS-4.2
Cryptosporidium hominis Chro.60409   ribonuclease PH-like protein
Cryptosporidium parvum cgd6_3540   archeo-eukaryotice exosomal RNAse PH
Dictyostelium discoideum DDB_G0271396   hypothetical protein
Drosophila melanogaster Dmel_CG8025   CG8025 gene product from transcript CG8025-RA
Echinococcus granulosus EgrG_000720150   Exosome complex exonuclease MTR3
Entamoeba histolytica EHI_166910   3 exoribonuclease family protein
Entamoeba histolytica EHI_126330   3 exoribonuclease family protein
Echinococcus multilocularis EmuJ_000720150   Exosome complex exonuclease MTR3
Homo sapiens 118460   exosome component 6
Leishmania braziliensis LbrM.35.5140   exosome-associated protein 4, putative
Leishmania donovani LdBPK_365120.1   exosome-associated protein 4, putative
Leishmania infantum LinJ.36.5120   exosome-associated protein 4, putative
Leishmania major LmjF.36.4895   exosome-associated protein 4, putative
Leishmania mexicana LmxM.36.4895   exosome-associated protein 4, putative
Loa Loa (eye worm) LOAG_05308   hypothetical protein
Mus musculus 72544   exosome component 6
Neospora caninum NCLIV_010510   3 exoribonuclease, putative
Oryza sativa 9269241   Os03g0844450
Oryza sativa 4344519   Os08g0116800
Plasmodium berghei PBANKA_0306300   3' exoribonuclease, putative
Plasmodium falciparum PF3D7_0209200   3'exoribonuclease, putative
Plasmodium knowlesi PKNH_0411900   3'exoribonuclease, putative
Plasmodium yoelii PY00320   hypothetical protein
Saccharomyces cerevisiae YGR158C   Mtr3p
Schistosoma japonicum Sjp_0025350   Exosome complex exonuclease MTR3, putative
Schistosoma japonicum Sjp_0310060   ko:K01149 exosome component 6 [EC:3.1.13.-], putative
Schistosoma mansoni Smp_120960.2   ribonuclease pH related
Schistosoma mansoni Smp_120960.3   ribonuclease pH related
Schistosoma mansoni Smp_120960.1   ribonuclease pH related
Schmidtea mediterranea mk4.000842.05   Exosome complex component MTR3
Trypanosoma brucei gambiense Tbg972.11.12360   exosome-associated protein 4, putative
Trypanosoma brucei Tb927.11.11030   exosome-associated protein 4
Trypanosoma congolense TcIL3000.11.11750   exosome-associated protein 4
Trypanosoma cruzi TcCLB.508269.60   exosome-associated protein 4, putative
Trypanosoma cruzi TcCLB.507841.34   exosome-associated protein 4, putative
Toxoplasma gondii TGME49_319650   3' exoribonuclease family, domain 1 domain-containing protein
Theileria parva TP01_1052   hypothetical protein
Trichomonas vaginalis TVAG_441560   conserved hypothetical protein

Essentiality

LmjF.36.4895 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.2820 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.2820 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.2820 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YGR158C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0306300 Plasmodium berghei Essential plasmo
TGME49_319650 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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

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

  • Lmaj006688AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj006688; Recombinant protein: full-length; Source: L major; exosome-associated protein 4, putative ;

Bibliographic References

No literature references available for this target.

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Gene identifier LmjF.36.4895 (Leishmania major), exosome-associated protein 4, putative
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