Detailed view for Tb927.4.3140

Basic information

TDR Targets ID: 16072
Trypanosoma brucei, Ribosome maturation protein SDO1
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.8005 | Length (AA): 468 | MW (Da): 51816 | 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

PF01172   Shwachman-Bodian-Diamond syndrome (SBDS) protein
PF09377   SBDS protein C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0042254   ribosome biogenesis and assembly  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (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
4 266 2kdo (A) 4 252 35.00 0 1 0.857269 0.97
15 247 2wbm (A) 5 224 18.00 0 1 0.683929 -0.02
16 256 1t95 (A) 12 239 18.00 0 1 0.73706 -0.17
294 327 2ytt (A) 2 35 18.00 0.3 0.02 0.419905 -1.74
294 327 2en6 (A) 2 35 15.00 0.58 0.01 0.399905 -1.85

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_127367)

Species Accession Gene Product
Arabidopsis thaliana AT1G43860   sequence-specific DNA binding transcription factor
Babesia bovis BBOV_IV005410   conserved hypothetical protein
Brugia malayi Bm1_44430   hypothetical protein
Candida albicans CaO19.10223   similar to S. cerevisiae YLR022C
Candida albicans CaO19.2708   similar to S. cerevisiae YLR022C
Caenorhabditis elegans CELE_W06E11.4   Protein SBDS-1
Cryptosporidium hominis Chro.80384   hypothetical protein
Cryptosporidium parvum cgd8_3310   S. cerevisiae Ylr022cp like protein that has a C2H2 zinc finger and is a component of the exosome
Dictyostelium discoideum DDB_G0272324   Shwachman-Bodian-Diamond syndrome protein
Drosophila melanogaster Dmel_CG8549   CG8549 gene product from transcript CG8549-RA
Echinococcus granulosus EgrG_000784400   ribosome maturation protein sbds
Entamoeba histolytica EHI_151360   hypothetical protein
Entamoeba histolytica EHI_179200   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000784400   ribosome maturation protein sbds
Giardia lamblia GL50803_22802   Shwachman-Bodian-Diamond syndrome protein-like protein
Giardia lamblia GL50803_40521   Hypothetical protein
Homo sapiens ENSG00000126524   Shwachman-Bodian-Diamond syndrome
Leishmania braziliensis LbrM.20.1140   hypothetical protein, conserved
Leishmania donovani LdBPK_341190.1   Shwachman-Bodian-Diamond syndrome (SBDS) protein/SBDS protein C-terminal domain containing protein, putative
Leishmania infantum LinJ.34.1190   hypothetical protein, conserved
Leishmania major LmjF.34.1110   hypothetical protein, conserved
Leishmania mexicana LmxM.33.1110   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04440   shwachman-Bodian-Diamond syndrome
Mus musculus ENSMUSG00000025337   Shwachman-Bodian-Diamond syndrome homolog (human)
Neospora caninum NCLIV_022460   zinc finger (C2H2 type) domain-containing protein, putative
Oryza sativa 4344458   Os08g0107500
Plasmodium berghei PBANKA_1031600   ribosome maturation protein SBDS, putative
Plasmodium falciparum PF3D7_1410900   ribosome maturation protein SBDS, putative
Plasmodium knowlesi PKNH_1347400   ribosome maturation protein SBDS, putative
Plasmodium vivax PVX_085905   ribosome maturation protein SBDS, putative
Plasmodium yoelii PY04031   unnamed protein product, putative
Saccharomyces cerevisiae YLR022C   Sdo1p
Schistosoma mansoni Smp_007970   hypothetical protein
Schmidtea mediterranea mk4.000545.02   Ribosome maturation protein SBDS
Trypanosoma brucei gambiense Tbg972.4.3150   hypothetical protein, conserved
Trypanosoma brucei Tb927.4.3140   Ribosome maturation protein SDO1
Trypanosoma cruzi TcCLB.504055.10   Shwachman-Bodian-Diamond syndrome (SBDS) protein/SBDS protein C-terminal domain containing protein, putative
Trypanosoma cruzi TcCLB.506265.209   Shwachman-Bodian-Diamond syndrome (SBDS) protein/SBDS protein C-terminal domain containing protein, putative
Toxoplasma gondii TGME49_202470   rRNA metabolism protein, SBDS family protein
Theileria parva TP01_0347   hypothetical protein, conserved
Trichomonas vaginalis TVAG_014970   conserved hypothetical protein
Trichomonas vaginalis TVAG_221140   conserved hypothetical protein
Trichomonas vaginalis TVAG_356750   conserved hypothetical protein
Trichomonas vaginalis TVAG_233330   conserved hypothetical protein

Essentiality

Tb927.4.3140 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.3140 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.3140 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.3140 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.4.3140 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YLR022C Saccharomyces cerevisiae inviable yeastgenome
TGME49_202470 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.

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 procyclic forms . 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 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
Species Known druggable target Linked compounds Reference
Saccharomyces cerevisiae Sdo1p Compounds References
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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Gene identifier Tb927.4.3140 (Trypanosoma brucei), Ribosome maturation protein SDO1
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