Detailed view for LmjF.34.3980

Basic information

TDR Targets ID: 28074
Leishmania major, nucleolar protein family a member-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.2302 | Length (AA): 148 | MW (Da): 16744 | 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

PF01248   Ribosomal protein L7Ae/L30e/S12e/Gadd45 family

Gene Ontology

Mouse over links to read term descriptions.
GO:1990904   GO:ribonucleoprotein complex  

GO:0042254   ribosome biogenesis and assembly  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (KEGG)

Structural information

Modbase 3D models:

There are 6 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
20 144 1zwz (A) 5 126 26.00 0 1 1.31 -1.69
32 144 2czw (A) 13 122 26.00 0 1 1.2 -2
18 144 2ozb (A) 3 126 31.00 0 1 1.34431 -1.39
23 144 5ewr (A) 25 143 27.00 0 1 1.30382 -1.82
27 146 2fc3 (A) 4 123 28.00 0 1 1.35001 -1.72
34 144 2lbw (A) 38 156 44.00 0 1 1.2806 -1.17

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 80-100% 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_128156)

Species Accession Gene Product
Arabidopsis thaliana AT5G08180   H/ACA ribonucleoprotein complex subunit 2-like protein
Babesia bovis BBOV_II004250   ribosomal protein L7Ae-related protein, putative
Brugia malayi Bm1_25650   Ribosomal protein L7Ae containing protein
Candida albicans CaO19.8159   similar to S. cerevisiae NHP2 (YDL208W) nucleolar protein in H/ACA snoRNPs involved in pseudouridinylation of rRNA
Candida albicans CaO19.526   similar to S. cerevisiae NHP2 (YDL208W) nucleolar protein in H/ACA snoRNPs involved in pseudouridinylation of rRNA
Caenorhabditis elegans CELE_Y48A6B.3   Protein Y48A6B.3
Cryptosporidium hominis Chro.30105   nucleolar protein, possibly involved in ribosomal RNA pseudouridinylation, in association with snRNAs
Cryptosporidium parvum cgd3_760   HMG-like nuclear protein, Nhp2p, pelota RNA binding domain containing protein
Dictyostelium discoideum DDB_G0289699   H/ACA RNP complex subunit 2
Drosophila melanogaster Dmel_CG5258   CG5258 gene product from transcript CG5258-RB
Echinococcus granulosus EgrG_001130800   H:ACA ribonucleoprotein complex subunit 2
Entamoeba histolytica EHI_001850   H/ACA ribonucleoprotein complex subunit 2-like protein, putative
Entamoeba histolytica EHI_102280   H/ACA ribonucleoprotein complex subunit 2-like protein, putative
Echinococcus multilocularis EmuJ_001130800   H:ACA ribonucleoprotein complex subunit 2
Giardia lamblia GL50803_13926   Nucleolar protein family A, member 2
Homo sapiens ENSG00000145912   NHP2 ribonucleoprotein
Leishmania braziliensis LbrM.20.3610   nucleolar protein family a member-like protein
Leishmania donovani LdBPK_343810.1   nucleolar protein family a member-like protein
Leishmania infantum LinJ.34.3810   nucleolar protein family a member-like protein
Leishmania major LmjF.34.3980   nucleolar protein family a member-like protein
Leishmania mexicana LmxM.33.3980   nucleolar protein family a member-like protein
Loa Loa (eye worm) LOAG_05088   hypothetical protein
Mus musculus ENSMUSG00000001056   NHP2 ribonucleoprotein
Neospora caninum NCLIV_056830   60S ribosomal protein L7a, putative
Oryza sativa 4340741   Os06g0274200
Oryza sativa 4330603   Os02g0728600
Plasmodium berghei PBANKA_0721900   60S ribosomal protein L7ae/L30e, putative
Plasmodium falciparum PF3D7_0419800   60S ribosomal protein L7ae/L30e, putative
Plasmodium knowlesi PKNH_0512500   60S ribosomal protein L7ae/L30e, putative
Plasmodium vivax PVX_090080   ribosomal protein L7Ae-related protein, putative
Saccharomyces cerevisiae YDL208W   snoRNA-binding protein NHP2
Schistosoma japonicum Sjp_0212590   H/ACA ribonucleoprotein complex subunit 2, putative
Schistosoma mansoni Smp_098330   nucleolar protein family A member
Schmidtea mediterranea mk4.001695.04   Putative H/ACA ribonucleoprotein complex subunit 2-like protein
Schmidtea mediterranea mk4.006644.01   Putative H/ACA ribonucleoprotein complex subunit 2-like protein
Trypanosoma brucei gambiense Tbg972.4.520   50S ribosomal protein L7Ae, putative
Trypanosoma brucei Tb927.4.750   50S ribosomal protein L7Ae, putative
Trypanosoma cruzi TcCLB.507053.10   50S ribosomal protein L7Ae, putative
Toxoplasma gondii TGME49_313560   60S ribosomal protein L7a, putative
Theileria parva TP04_0176   40S ribosomal protein L7Ae, putative
Trichomonas vaginalis TVAG_255390   H/ACA ribonucleoprotein complex subunit, putative

Essentiality

LmjF.34.3980 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.750 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.750 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.750 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.750 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y48A6B.3 Caenorhabditis elegans slow growth wormbase
YDL208W Saccharomyces cerevisiae inviable yeastgenome
TGME49_313560 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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.
  • 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

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.

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Gene identifier LmjF.34.3980 (Leishmania major), nucleolar protein family a member-like protein
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