Detailed view for Tb927.11.3070

Basic information

TDR Targets ID: 20194
Trypanosoma brucei, ribosome assembly protein RRB1, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.3015 | Length (AA): 576 | MW (Da): 64325 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG3

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

PF12265   Histone-binding protein RBBP4 or subunit C of CAF1 complex

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
9 143 5h78 (A) 28 162 8.00 0 0 0.423875 -1.37
110 562 3cfs (B) 7 396 25.00 0 1 0.815958 0.63
440 508 5kdo (B) 196 260 31.00 0.32 1 0.498992 -0.4
445 503 4lg8 (A) 367 421 42.00 0.0014 0.71 0.501631 0.11

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 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_128348)

Species Accession Gene Product
Arabidopsis thaliana AT2G19540   transducin family protein / WD-40 repeat family protein
Babesia bovis BBOV_II006970   WD domain, G-beta repeat containing protein
Brugia malayi Bm1_25005   Glutamate-rich WD-repeat protein 1
Candida albicans CaO19.6355   potential WD40 repeat protein similar to S. cerevisiae RRB1 (YMR131C) nucleolar protein involved in 60S ribosomal subunit assemb
Candida albicans CaO19.13712   potential WD40 repeat protein similar to S. cerevisiae RRB1 (YMR131C) nucleolar protein involved in 60S ribosomal subunit assemb
Caenorhabditis elegans CELE_Y54H5A.1   Protein Y54H5A.1
Cryptosporidium hominis Chro.40382   hypothetical protein
Cryptosporidium parvum cgd4_3360   WD repeat protein
Dictyostelium discoideum DDB_G0291566   glutamate-rich WD repeat-containing protein 1
Drosophila melanogaster Dmel_CG12792   lethal (2) 09851
Echinococcus granulosus EgrG_000630400   glutamate rich WD repeat containing protein
Entamoeba histolytica EHI_052160   WD domain containing protein
Echinococcus multilocularis EmuJ_000630400   glutamate rich WD repeat containing protein
Giardia lamblia GL50803_14174   Glutamate-rich WD-repeat protein
Homo sapiens 83743   glutamate-rich WD repeat containing 1
Leishmania braziliensis LbrM.33.2190   hypothetical protein, conserved
Leishmania donovani LdBPK_332020.1   ribosome assembly protein RRB1, putative
Leishmania infantum LinJ.33.2020   hypothetical protein, conserved
Leishmania major LmjF.33.1910   hypothetical protein, conserved
Leishmania mexicana LmxM.32.1910   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_12224   glutamate-rich WD-repeat protein 1
Mus musculus ENSMUSG00000053801   glutamate-rich WD repeat containing 1
Neospora caninum NCLIV_055640   Wd repeat protein, putative
Oryza sativa 4349700   Os11g0134500
Onchocerca volvulus OVOC9238   Lethal (2) 09851 homolog
Plasmodium berghei PBANKA_0714800   ribosome assembly protein RRB1, putative
Plasmodium falciparum PF3D7_0816000   ribosome assembly protein RRB1, putative
Plasmodium knowlesi PKNH_0504400   ribosome assembly protein RRB1, putative
Plasmodium vivax PVX_089605   WD domain, G-beta repeat domain containing protein
Plasmodium yoelii PY00572   putative WD-40 repeat protein
Saccharomyces cerevisiae YMR131C   Rrb1p
Schistosoma japonicum Sjp_0301730   Glutamate-rich WD repeat-containing protein 1, putative
Schistosoma mansoni Smp_022660   hypothetical protein
Schmidtea mediterranea mk4.000703.02   Putative wd-repeat protein
Trypanosoma brucei gambiense Tbg972.11.3390   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.3070   ribosome assembly protein RRB1, putative
Trypanosoma congolense TcIL3000.11.2830   ribosome assembly protein RRB1, putative
Trypanosoma cruzi TcCLB.510431.220   ribosome assembly protein RRB1, putative
Toxoplasma gondii TGME49_311870   WD domain, G-beta repeat-containing protein
Theileria parva TP02_0670   hypothetical protein
Trichomonas vaginalis TVAG_434020   WD-repeat protein, putative

Essentiality

Tb927.11.3070 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.0570 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.0570 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.0570 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.0570 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y54H5A.1 Caenorhabditis elegans embryonic lethal wormbase
YMR131C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0714800 Plasmodium berghei Essential plasmo
TGME49_311870 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) 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: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) 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 procyclic forms . 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.

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User comments

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Gene identifier Tb927.11.3070 (Trypanosoma brucei), ribosome assembly protein RRB1, putative
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