Detailed view for Tb927.9.13340

Basic information

TDR Targets ID: 18880
Trypanosoma brucei, Nop53 (60S ribosomal biogenesis), putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 11.1784 | Length (AA): 311 | MW (Da): 35951 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF07767   Nop53 (60S ribosomal biogenesis)

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 3 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
65 223 4uos (A) 21 185 16.00 0 0.4 0.761054 -1.34
73 223 4phq (B) 71 235 13.00 0 0.15 0.619731 -0.42
146 226 4kzy (G) 146 235 37.00 0.88 0.22 0.34035 1.14

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 Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_129039)

Species Accession Gene Product
Arabidopsis thaliana AT2G40430   hypothetical protein
Brugia malayi Bm1_52230   Glioma tumor suppressor candidate region gene 2 protein
Candida albicans CaO19.14175   similar to S. cerevisiae YPL146C potential nucleolar protein
Candida albicans CaO19.6886   similar to S. cerevisiae YPL146C potential nucleolar protein
Caenorhabditis elegans CELE_Y39B6A.33   Protein Y39B6A.33
Dictyostelium discoideum DDB_G0267572   hypothetical protein
Drosophila melanogaster Dmel_CG1785   CG1785 gene product from transcript CG1785-RA
Echinococcus granulosus EgrG_000199300   expressed conserved protein
Echinococcus multilocularis EmuJ_000199300   expressed conserved protein
Giardia lamblia GL50803_8415   Hypothetical protein
Homo sapiens ENSG00000105373   glioma tumor suppressor candidate region gene 2
Leishmania braziliensis LbrM.34.2420   hypothetical protein, conserved
Leishmania donovani LdBPK_352520.1   Nop53 (60S ribosomal biogenesis), putative
Leishmania infantum LinJ.35.2520   hypothetical protein, conserved
Leishmania major LmjF.35.2480   hypothetical protein, conserved
Leishmania mexicana LmxM.34.2480   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_02068   hypothetical protein
Loa Loa (eye worm) LOAG_09292   hypothetical protein
Mus musculus ENSMUSG00000041560   glioma tumor suppressor candidate region gene 2
Oryza sativa 4337783   Os05g0144200
Onchocerca volvulus OVOC6491   Glioma tumor suppressor candidate region gene 2 protein homolog
Saccharomyces cerevisiae YPL146C   Nop53p
Schistosoma japonicum Sjp_0098640   expressed protein
Schistosoma mansoni Smp_083680   hypothetical protein
Trypanosoma brucei gambiense Tbg972.9.8330   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.13340   Nop53 (60S ribosomal biogenesis), putative
Trypanosoma congolense TcIL3000_0_21920   Nop53 (60S ribosomal biogenesis), putative
Trypanosoma cruzi TcCLB.510657.90   Nop53 (60S ribosomal biogenesis), putative
Trypanosoma cruzi TcCLB.510747.140   Nop53 (60S ribosomal biogenesis), putative

Essentiality

Tb927.9.13340 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4190 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.4190 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.4190 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.4190 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y39B6A.33 Caenorhabditis elegans larval arrest wormbase
CELE_Y39B6A.33 Caenorhabditis elegans slow growth wormbase
YPL146C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Tb927.9.13340 (Trypanosoma brucei), Nop53 (60S ribosomal biogenesis), putative
Title for this comment
Comment