Detailed view for LmjF.35.2550

Basic information

TDR Targets ID: 22809
Leishmania major, RNA binding protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 10.6175 | Length (AA): 455 | MW (Da): 50435 | 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

PF00076   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide 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
150 349 1fje (B) 3 173 29.00 0.0000026 1 0.52 0.97
272 330 1x4e (A) 8 64 28.00 0.00000038 0.72 0.57 -1.34
162 362 4n0t (A) 42 211 26.00 0.13 1 0.468258 0.33
267 344 3ucg (A) 169 244 33.00 0 1 0.722529 -1.7
271 330 2mzr (A) 162 217 43.00 0.00091 0.97 0.623368 -0.45

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 metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile amastigotes. 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_128354)

Species Accession Gene Product
Arabidopsis thaliana AT5G46840   RNA recognition motif-containing protein
Babesia bovis BBOV_III009290   RNA recognition motif domain containing protein
Brugia malayi Bm1_37250   RNA recognition motif.
Candida albicans CaO19.8429   nucleolar protein
Candida albicans CaO19.809   nucleolar protein
Caenorhabditis elegans CELE_F11A10.7   Protein F11A10.7
Cryptosporidium hominis Chro.30395   hypothetical protein
Cryptosporidium parvum cgd3_3500   Nop12p nucleolar protein, RRM domain
Dictyostelium discoideum DDB_G0289941   hypothetical protein
Drosophila melanogaster Dmel_CG12288   CG12288 gene product from transcript CG12288-RA
Echinococcus granulosus EgrG_000762400   RNA binding protein 34
Entamoeba histolytica EHI_137710   RNA recognition motif domain containing protein
Echinococcus multilocularis EmuJ_000762400   RNA binding protein 34
Homo sapiens ENSG00000188739   RNA binding motif protein 34
Leishmania braziliensis LbrM.34.2480   RNA binding protein, putative
Leishmania donovani LdBPK_352590.1   Double RNA binding domain protein 9
Leishmania infantum LinJ.35.2590   RNA binding protein, putative
Leishmania major LmjF.35.2550   RNA binding protein, putative
Leishmania mexicana LmxM.34.2550   RNA binding protein, putative
Loa Loa (eye worm) LOAG_04878   RNA recognition domain-containing protein
Mus musculus ENSMUSG00000033931   RNA binding motif protein 34
Neospora caninum NCLIV_028890   hypothetical protein
Oryza sativa 4334825   Os03g0854300
Plasmodium berghei PBANKA_0504200   RNA-binding protein 34, putative
Plasmodium falciparum PF3D7_1020000   RNA-binding protein 34, putative
Plasmodium knowlesi PKNH_0604200   RNA-binding protein 34, putative
Plasmodium vivax PVX_001865   RNA-binding protein, putative
Plasmodium yoelii PY00605   KED
Saccharomyces cerevisiae YOL041C   Nop12p
Schistosoma japonicum Sjp_0024100   RNA-binding protein 34, putative
Schistosoma mansoni Smp_130190   RNA binding protein
Schmidtea mediterranea mk4.000024.16   RNA-binding protein 34
Trypanosoma brucei gambiense Tbg972.9.8260   RNA-binding protein, putative,DRBD9
Trypanosoma brucei Tb927.9.13280   Double RNA binding domain protein 9
Trypanosoma congolense TcIL3000_9_5600   Double RNA binding domain protein 9
Trypanosoma cruzi TcCLB.510657.160   Double RNA binding domain protein 9
Trypanosoma cruzi TcCLB.510747.80   Double RNA binding domain protein 9
Toxoplasma gondii TGME49_283882   hypothetical protein
Theileria parva TP04_0838   hypothetical protein, conserved
Trichomonas vaginalis TVAG_108440   ribonucleoprotein, putative

Essentiality

LmjF.35.2550 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4120 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.4120 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.4120 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.4120 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F11A10.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_F11A10.7 Caenorhabditis elegans larval arrest wormbase
CELE_F11A10.7 Caenorhabditis elegans sterile wormbase
TGME49_283882 Toxoplasma gondii Probably essential sidik
TGME49_283882 Toxoplasma gondii Essentiality uncertain 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.
  • 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.
  • 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

  • Lmaj00499AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj00499; Recombinant protein: full-length; Source: L major; hypothetical protein, conserved ;

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.35.2550 (Leishmania major), RNA binding protein, putative
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