Detailed view for Tb927.8.2450

Basic information

TDR Targets ID: 15818
Trypanosoma brucei, 5'-AMP-activated protein kinase subunit beta
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.4006 | Length (AA): 310 | MW (Da): 34492 | 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

PF04739   5'-AMP-activated protein kinase beta subunit, interaction domain
PF16561   Glycogen recognition site of AMP-activated protein kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0045859   regulation of protein kinase activity  
GO:0031588   AMP-activated protein kinase complex  
GO:0005515   protein binding  
GO:0007165   signal transduction  

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
88 303 5iso (D) 78 270 28.00 0 0.86 0.640574 1.54
105 158 4aef (A) 26 81 17.00 0.09 0.53 0.386994 -0.28
209 301 2v8q (B) 190 270 37.00 0 0.14 0.0814 1.73

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_127587)

Species Accession Gene Product
Arabidopsis thaliana AT4G16360   SNF1-related protein kinase regulatory subunit beta-2
Arabidopsis thaliana AT2G28060   5'-AMP-activated protein kinase beta-2 subunit protein
Babesia bovis BBOV_IV004160   hypothetical protein
Brugia malayi Bm1_05525   5'-AMP-activated protein kinase, beta subunit, complex-interacting region containing protein
Brugia malayi Bm1_18185   5'-AMP-activated protein kinase, beta subunit, complex-interacting region containing protein
Candida albicans CaO19.4084   glucose repression
Candida albicans CaO19.11565   glucose repression
Caenorhabditis elegans CELE_F55F3.1   Protein AAKB-1
Caenorhabditis elegans CELE_Y47D3A.15   Protein AAKB-2
Cryptosporidium hominis Chro.60240   gal83 protein
Cryptosporidium parvum cgd6_2050   AMP-activated protein kinase beta chain (has isoamylase N-terminal domain)
Dictyostelium discoideum DDB_G0281089   AMP-activated protein kinase beta subunit
Drosophila melanogaster Dmel_CG8057   alicorn
Echinococcus granulosus EgrG_000423400   AMPK beta subunit
Echinococcus multilocularis EmuJ_000423400   AMPK beta subunit
Giardia lamblia GL50803_101919   5-AMP-activated protein kinase, beta-1 subunit
Homo sapiens ENSG00000111725   protein kinase, AMP-activated, beta 1 non-catalytic subunit
Homo sapiens ENSG00000131791   protein kinase, AMP-activated, beta 2 non-catalytic subunit
Leishmania braziliensis LbrM.23.0520   hypothetical protein, conserved
Leishmania donovani LdBPK_230530.1   5'-AMP-activated protein kinase subunit beta, putative
Leishmania infantum LinJ.23.0530   hypothetical protein, conserved
Leishmania major LmjF.23.0490   hypothetical protein, conserved
Leishmania mexicana LmxM.23.0490   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_06268   5'-AMP-activated protein kinase
Mus musculus ENSMUSG00000038205   protein kinase, AMP-activated, beta 2 non-catalytic subunit
Mus musculus ENSMUSG00000029513   protein kinase, AMP-activated, beta 1 non-catalytic subunit
Neospora caninum NCLIV_037390   hypothetical protein
Oryza sativa 4344345   Os07g0687300
Onchocerca volvulus OVOC2137   Alicorn homolog
Saccharomyces cerevisiae YGL208W   Sip2p
Saccharomyces cerevisiae YER027C   Gal83p
Schistosoma japonicum Sjp_0128580   expressed protein
Schistosoma mansoni Smp_170160   protein kinase subunit beta
Schmidtea mediterranea mk4.013965.02   Alicorn
Schmidtea mediterranea mk4.010607.00  
Schmidtea mediterranea mk4.013518.02  
Schmidtea mediterranea mk4.026301.00  
Schmidtea mediterranea mk4.023206.00  
Schmidtea mediterranea mk4.037975.00  
Schmidtea mediterranea mk4.015150.00  
Schmidtea mediterranea mk4.016300.03   Alicorn
Schmidtea mediterranea mk4.042077.00  
Trypanosoma brucei gambiense Tbg972.8.1900   hypothetical protein, conserved
Trypanosoma brucei Tb927.8.2450   5'-AMP-activated protein kinase subunit beta
Trypanosoma cruzi TcCLB.504427.50   SNF1-related protein kinase regulatory subunit beta, putative
Trypanosoma cruzi TcCLB.509331.90   5'-AMP-activated protein kinase subunit beta, putative
Toxoplasma gondii TGME49_268960   5'-AMP-activated protein kinase subunit beta-1 family protein, putative
Theileria parva TP01_0339   hypothetical protein

Essentiality

Tb927.8.2450 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.2450 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.2450 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.2450 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.2450 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_268960 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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 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

Druggability index (range: 0 to 1): 0.3

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
Homo sapiens protein kinase, AMP-activated, beta 1 non-catalytic subunit Compounds References
Homo sapiens protein kinase, AMP-activated, beta 2 non-catalytic subunit Compounds References
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
0.0068 0.3524 1
0.0137 0.2567 1
0.0809898 0.314459 0.423874
0.0067 0.3524 1
0.359463 0.317299 0.385786
0.00932008 0.323325 0.623386
0.0137 1 0.5
0.0809898 0.314459 0.423874
0.0809898 0.314459 0.423874
0.0192 0.3043 1
0.0056 0.3524 1

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.

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Gene identifier Tb927.8.2450 (Trypanosoma brucei), 5'-AMP-activated protein kinase subunit beta
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