Detailed view for LmjF.34.4290

Basic information

TDR Targets ID: 27296
Leishmania major, nucleolar protein family a, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 11.9125 | Length (AA): 220 | MW (Da): 21926 | 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

PF04410   Gar1/Naf1 RNA binding region

Gene Ontology

Mouse over links to read term descriptions.
GO:0031429   box H/ACA snoRNP complex  
GO:0005732   small nucleolar ribonucleoprotein complex  
GO:0019843   rRNA binding  
GO:0042254   ribosome biogenesis and assembly  
GO:0006364   rRNA processing  
GO:0001522   pseudouridine synthesis  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (KEGG)

Structural information

Modbase 3D models:

There are 2 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
6 46 3bog (C) 3 79 70.00 0.00000011 0.2 0.826964 -0.3
53 145 3u28 (C) 33 124 41.00 0 1 1.03003 -1.24

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 metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_128232)

Species Accession Gene Product
Arabidopsis thaliana AT5G18180   H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 protein
Arabidopsis thaliana AT3G03920   H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 protein
Babesia bovis BBOV_II002170   gar1 protein RNA binding region containing protein
Brugia malayi Bm1_39105   snoRNP protein GAR1
Candida albicans CaO19.8757   Small nucleolar RNP protein
Candida albicans CaO19.1164   small nucleolar RNP protein
Caenorhabditis elegans CELE_Y66H1A.4   Protein Y66H1A.4
Cryptosporidium hominis Chro.50206   small nucleolar RNP proteins; Gar1p
Cryptosporidium parvum cgd5_1760   small nucleolar RNP protein , Gar1 protein RNA binding region
Dictyostelium discoideum DDB_G0279013   Gar1 family protein
Drosophila melanogaster Dmel_CG4038   CG4038 gene product from transcript CG4038-RA
Echinococcus granulosus EgrG_000599100   H:ACA ribonucleoprotein complex subunit
Entamoeba histolytica EHI_194040   snoRNP protein gar1, putative
Echinococcus multilocularis EmuJ_000599100   H:ACA ribonucleoprotein complex subunit
Giardia lamblia GL50803_8794   Nucleolar GAR1-like protein, putative
Homo sapiens ENSG00000109534   GAR1 ribonucleoprotein
Leishmania braziliensis LbrM.20.3910   nucleolar protein family a, putative
Leishmania infantum LinJ.34.4120   nucleolar protein family a, putative
Leishmania major LmjF.34.4290   nucleolar protein family a, putative
Leishmania mexicana LmxM.33.4290   nucleolar protein family a, putative
Loa Loa (eye worm) LOAG_03932   snoRNP protein GAR1
Mus musculus ENSMUSG00000028010   GAR1 ribonucleoprotein homolog (yeast)
Neospora caninum NCLIV_035140   hypothetical protein
Oryza sativa 4350782   Os11g0579800
Plasmodium berghei PBANKA_1408000   H/ACA ribonucleoprotein complex subunit 1, putative
Plasmodium falciparum PF3D7_1309500   H/ACA ribonucleoprotein complex subunit 1, putative
Plasmodium knowlesi PKNH_1409900   H/ACA ribonucleoprotein complex subunit 1, putative
Plasmodium vivax PVX_122305   H/ACA ribonucleoprotein complex subunit 1, putative
Plasmodium yoelii PY02326   snornp protein gar1
Saccharomyces cerevisiae YHR089C   H/ACA snoRNP pseudouridylase subunit GAR1
Schistosoma japonicum Sjp_0113070   ko:K00998 phosphatidylserine synthase [EC2.7.8.8], putative
Schistosoma mansoni Smp_022730   nucleolar protein family A member 1 (snornp protein gar1)
Schmidtea mediterranea mk4.003228.02   Probable H/ACA ribonucleoprotein complex subunit 1-like protein
Trypanosoma brucei gambiense Tbg972.4.220   snoRNP protein GAR1, putative
Trypanosoma brucei Tb927.4.470   snoRNP protein GAR1, putative
Trypanosoma cruzi TcCLB.510687.120   snoRNP protein GAR1, putative
Toxoplasma gondii TGME49_272010   Gar1 protein RNA binding region protein
Theileria parva TP04_0350   small nuclear ribonucleoprotein gar1, putative
Trichomonas vaginalis TVAG_440180   H/ACA ribonucleoprotein complex subunit, putative

Essentiality

LmjF.34.4290 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.470 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.470 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.470 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.470 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y66H1A.4 Caenorhabditis elegans slow growth wormbase
CELE_Y66H1A.4 Caenorhabditis elegans sterile wormbase
PBANKA_1408000 Plasmodium berghei Essential plasmo
TGME49_272010 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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.

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Gene identifier LmjF.34.4290 (Leishmania major), nucleolar protein family a, putative
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