Detailed view for Tb927.11.11110

Basic information

TDR Targets ID: 13938
Trypanosoma brucei, Serine/threonine-protein kinase NEK20, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.7264 | Length (AA): 368 | MW (Da): 41695 | Paralog Number: 0

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

Druggability Group : DG4

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

PF00069   Protein kinase domain
PF08239   Bacterial SH3 domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0005524   ATP binding  
GO:0004713   protein tyrosine kinase activity  
GO:0004674   protein serine/threonine kinase activity  
GO:0004672   protein kinase activity  
GO:0006468   protein amino acid phosphorylation  

Structural information

Modbase 3D models:

There are 10 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
13 60 3b5x (A) 142 185 39.00 0.79 0.13 0.382793 3.37
6 368 5iso (C) 10 398 26.00 0 1 1.04031 0.42
8 285 4b9d (A) 0 275 27.00 0 1 1.00633 -0.85
10 361 5t6a (A) 49 427 23.00 0 1 1.20852 -0.05
12 154 2a19 (C) 267 435 40.00 0 0.88 0.521787 1.27
5 208 5h7c (A) 163 382 14.00 0.81 0.36 0.256435 -0.14
210 1175 4hzk (A) 68 1069 13.00 0 1 0.663607 0.14
764 973 3pdy (A) 545 746 13.00 0 0.86 0.285297 -2.06
788 957 5cwh (A) 6 159 42.00 0.000038 1 0.516412 -1.34
1004 1180 4uos (A) 6 177 31.00 0.000012 1 0.507202 -1.79

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_148164)

Species Accession Gene Product
Leishmania braziliensis LbrM.28.3220   protein kinase, putative
Leishmania donovani LdBPK_283240.1   serine/threonine kinase, putative
Leishmania infantum LinJ.28.3240   protein kinase, putative
Leishmania major LmjF.28.3000   protein kinase, putative
Leishmania mexicana LmxM.28.3000   protein kinase, putative
Trypanosoma brucei gambiense Tbg972.11.12430   protein kinase, putative,serine/threonine kinase, putative
Trypanosoma brucei Tb927.11.11110   Serine/threonine-protein kinase NEK20, putative
Trypanosoma congolense TcIL3000.11.11770   serine/threonine kinase, putative
Trypanosoma cruzi TcCLB.511671.80   Serine/threonine-protein kinase NEK20, putative
Trypanosoma cruzi TcCLB.508831.110   Serine/threonine-protein kinase NEK20, putative

Essentiality

Tb927.11.11110 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2900 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.2900 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.2900 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.2900 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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 3 days). References: 21363968
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) 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

Druggability index (range: 0 to 1): 0.5

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0027 1 0.5
0.0067 0.5 0.5
0.0016 0.5 0.5
0.0066 0.3101 0
0.0026 0.5 0.5
0.0039 0.5 0.5
0.0061 0.6883 0.5304
0.0036 0.5 0.5
0.0023 0.5 0.5
0.0007 0.5 0.5
0.0039 0.9485 0.5
0.0098 0.3242 0.2614
0.0008 0.5 0.5
0.0092 1 0.5
0.0029 0.5 0.5
0.0011 1 0.5
0.0062 0.6935 0
0.0059 1 1
0.0063 1 0.5
0.0033 0.5 0.5
0.0004 0.5 0.5
0.0081 0.5 0.5
0.0091 1 0.5
0.0007 0.5 0.5
0.0042 0.5 0.5
0.0018 0.5 0.5
0.0069 0.3067 1
0.0059 1 1
0.0032 0.5 0.5
0.0039 0.5 0.5
0.0037 1 0.5
0.0012 0.5 0.5
0.0003 0.5 0.5
0.0012 0.5 0.5
0.0012 0.5 0.5
0.0016 0.5 0.5
0.0033 1 0.5
0.0007 0.5 0.5
0.0063 0.7244 0.2543
0.0059 1 1
0.0022 0.5 0.5
0.0064 0.3377 0
0.0088 0.4477 0.5
0.0081 1 0.5
0.0056 1 0.5
0.0093 0.8828 0
0.0032 0.5 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

27 literature references were collected for this gene.

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Gene identifier Tb927.11.11110 (Trypanosoma brucei), Serine/threonine-protein kinase NEK20, putative
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