Detailed view for Tb927.6.4990

Basic information

TDR Targets ID: 10625
Trypanosoma brucei, mitochondrial ATP synthase delta chain
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.5371 | Length (AA): 182 | MW (Da): 20147 | Paralog Number: 0

Signal peptide: Y | 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

PF02823   ATP synthase, Delta/Epsilon chain, beta-sandwich domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0046933   hydrogen ion transporting ATP synthase activity, rotational mechanism  
GO:0045261   proton-transporting ATP synthase complex, catalytic core F(1)  
GO:0015986   ATP synthesis coupled proton transport  

Metabolic Pathways

Oxidative phosphorylation (KEGG)
Global map (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
47 180 2e5y (A) 1 131 22.00 0.000000000013 1 1.07166 -0.47
49 179 2v7q (H) 15 145 32.00 0 1 1.17618 -0.48
56 124 5dn6 (I) 10 77 40.00 0.18 0.89 0.884521 -0.38

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:

PDB tag
  • 6F5D:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

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_127404)

Species Accession Gene Product
Arabidopsis thaliana ArthCp028   ATP synthase epsilon chain
Arabidopsis thaliana AT5G47030   ATP synthase subunit delta'
Babesia bovis BBOV_III004400   ATP synthase, Delta/Epsilon chain, beta-sandwich domain containing protein
Brugia malayi Bm1_57260   ATP synthase delta chain, mitochondrial precursor, putative
Candida albicans CaO19.7678   ATP synthase delta subunit
Caenorhabditis elegans CELE_F58F12.1   Protein F58F12.1
Dictyostelium discoideum DDB_G0269038   ATP synthase F1 delta
Drosophila melanogaster Dmel_CG2968   lethal (1) G0230
Escherichia coli b3731   F1 sector of membrane-bound ATP synthase, epsilon subunit
Echinococcus granulosus EgrG_000656000   5'partial|ATP synthase subunit delta mitochondrial
Echinococcus multilocularis EmuJ_000656000   ATP synthase subunit delta, mitochondrial
Homo sapiens ENSG00000099624   ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit
Leishmania braziliensis LbrM.30.3630   ATP synthase, epsilon chain, putative
Leishmania donovani LdBPK_303660.1   ATP synthase, epsilon chain, putative
Leishmania infantum LinJ.30.3660   ATP synthase, epsilon chain, putative
Leishmania major LmjF.30.3600   ATP synthase, epsilon chain, putative
Leishmania mexicana LmxM.29.3600   ATP synthase, epsilon chain, putative
Loa Loa (eye worm) LOAG_04001   ATP synthase subunit delta
Mycobacterium leprae ML1146   PROBABLE ATP SYNTHASE EPSILON CHAIN ATPC
Mus musculus ENSMUSG00000003072   ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit
Mycobacterium tuberculosis Rv1311   Probable ATP synthase epsilon chain AtpC
Mycobacterium ulcerans MUL_3953   F0F1 ATP synthase subunit epsilon
Neospora caninum NCLIV_046830   ATP synthase, putative
Oryza sativa 4343288   Os07g0495200
Onchocerca volvulus OVOC9964   ATP synthase subunit delta, mitochondrial homolog
Plasmodium berghei PBANKA_0901400   ATP synthase subunit delta, mitochondrial, putative
Plasmodium falciparum PF3D7_1147700   ATP synthase subunit delta, mitochondrial, putative
Plasmodium knowlesi PKNH_0945600   ATP synthase subunit delta, mitochondrial, putative
Plasmodium vivax PVX_092970   hypothetical protein, conserved
Plasmodium yoelii PY05978   hypothetical protein
Saccharomyces cerevisiae YDL004W   F1F0 ATP synthase subunit delta
Schistosoma japonicum Sjp_0082240   ko:K02134 F-type H+-transporting ATPase delta chain, putative
Schistosoma mansoni Smp_082120   ATP synthase delta chain mitochondrial
Schmidtea mediterranea mk4.000215.15   ATP synthase subunit delta, mitochondrial
Trypanosoma brucei gambiense Tbg972.6.4790   ATP synthase, epsilon chain, putative
Trypanosoma brucei Tb927.6.4990   mitochondrial ATP synthase delta chain
Trypanosoma congolense TcIL3000_6_4420   ATP synthase, epsilon chain, putative
Trypanosoma cruzi TcCLB.506945.240   ATP synthase, epsilon chain, putative
Toxoplasma gondii TGME49_226000   ATP synthase, putative
Theileria parva TP02_0253   ATP synthase F1, delta subunit, putative
Wolbachia endosymbiont of Brugia malayi Wbm0688   ATP synthase F0F1 subunit epsilon

Essentiality

Tb927.6.4990 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1333 Mycobacterium tuberculosis essential nmpdr
Tb927.6.4990 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.4990 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.4990 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.4990 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3731 Escherichia coli non-essential goodall
CELE_F58F12.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_F58F12.1 Caenorhabditis elegans larval arrest wormbase
CELE_F58F12.1 Caenorhabditis elegans slow growth wormbase
YDL004W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0901400 Plasmodium berghei Slow plasmo
TGME49_226000 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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.

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

  • Validation: inhibited in cell-free system. As observed in: T. b. brucei.Evidence: inferred from specific protein inhibition
  • annotated by: ts4@sanger.ac.uk.
  • References: 8806783

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
Mycobacterium tuberculosis Probable ATP synthase epsilon chain AtpC 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
0.0116 0.2795 0.4589
0.0183 0.4018 0.645

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

6 literature references were 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 Tb927.6.4990 (Trypanosoma brucei), mitochondrial ATP synthase delta chain
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