Detailed view for Tb927.11.4130

Basic information

TDR Targets ID: 15373
Trypanosoma brucei, ubiquitin-like protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.8256 | Length (AA): 620 | MW (Da): 67283 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00240   Ubiquitin family

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 17 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
1 169 3b08 (A) 1 140 29.00 0 1 0.432981 0.01
2 75 5hpl (C) 0 75 32.00 0.00015 1 0.674555 -1.63
13 73 1bt0 (A) 7 72 34.00 0.0096 0.94 0.502587 -0.58
19 80 1wh3 (A) 24 86 23.00 0.000083 0.99 0.4534 -0.43
153 189 5d60 (A) 173 212 19.00 0 0.03 0.432477 -2.79
350 408 5mq9 (A) 103 173 36.00 0.39 0.48 0.418361 -0.33
20 109 5b04 (E) 38 120 27.00 0.000088 0.87 0.444672 -0.51
21 95 2ggo (A) 1 67 22.00 0.0000019 0.37 0.24071 0.01
50 508 5b04 (I) 39 442 27.00 0 1 0.732435 0.91
386 550 1hm9 (A) 285 440 26.00 0.76 0.94 0.507981 -0.31
398 548 3t57 (A) 49 210 28.00 0.00018 1 0.467483 0.05
400 465 4n27 (A) 74 129 41.00 0.02 1 0.439032 -0.11
409 477 5vmk (A) 254 324 33.00 0.57 1 0.601425 -0.99
438 478 3d98 (A) 351 391 27.00 0 0.65 0.418329 -0.44
532 582 3r8y (A) 166 219 20.00 0.42 0.08 0.209571 0.08
590 653 3jui (A) 542 604 13.00 0.00069 0.02 0.316604 -1.16
600 681 1paq (A) 544 634 15.00 0.0061 0.04 0.245959 -0.87

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_145896)

Species Accession Gene Product
Leishmania braziliensis LbrM.13.0550   ubiquitin-like protein
Leishmania donovani LdBPK_130620.1   ubiquitin-like protein
Leishmania infantum LinJ.13.0620   ubiquitin-like protein
Leishmania major LmjF.13.0730   ubiquitin-like protein
Leishmania mexicana LmxM.13.0730   ubiquitin-like protein
Trypanosoma brucei gambiense Tbg972.11.4720   ubiquitin-like protein, putative
Trypanosoma brucei Tb927.11.4130   ubiquitin-like protein, putative
Trypanosoma congolense TcIL3000.11.4170   ubiquitin-like protein, putative
Trypanosoma cruzi TcCLB.511855.20   ubiquitin-like protein, putative
Trypanosoma cruzi TcCLB.506737.70   ubiquitin-like protein, putative

Essentiality

Tb927.11.4130 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.1600 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.1600 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.1600 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.1600 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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) 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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Gene identifier Tb927.11.4130 (Trypanosoma brucei), ubiquitin-like protein, putative
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