Detailed view for Tb927.3.2840

Basic information

TDR Targets ID: 15644
Trypanosoma brucei, inorganic pyrophosphatase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.7355 | Length (AA): 261 | MW (Da): 28676 | 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

PF00719   Inorganic pyrophosphatase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0004427   inorganic diphosphatase activity  
GO:0000287   magnesium ion binding  
GO:0006796   phosphate metabolic process  

Metabolic Pathways

Oxidative phosphorylation (KEGG)

Structural information

Modbase 3D models:

There are 4 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
10 256 5c5v (A) 153 413 37.00 0 1 1.34616 -0.62
20 260 1e9g (A) 1 242 38.00 0 1 1.42117 -0.9
24 249 5cux (A) 171 406 41.00 0 1 1.3429 -0.68
50 245 1twl (A) 2 170 30.00 0 1 1.02496 -0.64

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
Mid 40-60% percentile Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 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_128875)

Species Accession Gene Product
Arabidopsis thaliana AT1G01050   pyrophosphorylase 1
Arabidopsis thaliana AT2G18230   soluble inorganic pyrophosphatase 2
Arabidopsis thaliana AT2G46860   pyrophosphorylase 3
Arabidopsis thaliana AT4G01480   pyrophosphorylase 5
Arabidopsis thaliana AT3G53620   pyrophosphorylase 4
Chlamydia trachomatis CT_772   inorganic pyrophosphatase
Escherichia coli b4226   inorganic pyrophosphatase
Leishmania braziliensis LbrM.03.0820   inorganic pyrophosphatase, putative
Leishmania donovani LdBPK_030890.1   inorganic pyrophosphatase, putative
Leishmania infantum LinJ.03.0890   inorganic pyrophosphatase, putative
Leishmania major LmjF.03.0910   inorganic pyrophosphatase, putative
Leishmania mexicana LmxM.03.0910   inorganic pyrophosphatase, putative
Mycobacterium leprae ML0210c   Probable inorganic pyrophosphatase Ppa (pyrophosphate phospho-hydrolase_ (PPase) (inorganic diphosphatase) (Diphosphate phospho-
Mycobacterium tuberculosis Rv3628   Inorganic pyrophosphatase Ppa (pyrophosphate phospho-hydrolase) (PPASE) (inorganic diphosphatase) (diphosphate phospho-hydrolase
Mycobacterium ulcerans MUL_4204   inorganic pyrophosphatase Ppa
Oryza sativa 4337476   Os04g0687100
Oryza sativa 4325072   Os01g0866500
Oryza sativa 4330457   Os02g0704900
Oryza sativa 4337608   Os05g0114000
Oryza sativa 4348583   Os10g0406100
Oryza sativa 9272240   Os01g0322300
Oryza sativa 4338911   Os05g0438500
Trypanosoma brucei gambiense Tbg972.3.2910   inorganic pyrophosphatase, putative
Trypanosoma brucei Tb927.3.2840   inorganic pyrophosphatase, putative
Trypanosoma congolense TcIL3000_3_1740   inorganic pyrophosphatase, putative
Trypanosoma cruzi TcCLB.508181.140   inorganic pyrophosphatase, putative
Trypanosoma cruzi TcCLB.508153.820   inorganic pyrophosphatase, putative
Trichomonas vaginalis TVAG_012660   inorganic pyrophosphatase, putative
Trichomonas vaginalis TVAG_019690   inorganic pyrophosphatase, putative
Trichomonas vaginalis TVAG_472200   inorganic pyrophosphatase, putative
Trichomonas vaginalis TVAG_231330   inorganic pyrophosphatase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0583   inorganic pyrophosphatase

Essentiality

Tb927.3.2840 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.2840 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.2840 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.2840 this record Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.3.2840 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4226 Escherichia coli essential goodall
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) 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: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
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) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant 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
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

  • Assay for Inorganic Pyrophosphatase (3.6.1.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Trypanosoma brucei ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Tb927.3.2840 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Trypanosoma brucei ( 1 )

Bibliographic References

9 literature references were collected for this gene.

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Gene identifier Tb927.3.2840 (Trypanosoma brucei), inorganic pyrophosphatase, putative
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