Detailed view for Tb927.8.1720

Basic information

TDR Targets ID: 13299
Trypanosoma brucei, phosphatidylglycerolphosphate synthase, mitochondrial
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.1191 | Length (AA): 615 | MW (Da): 68120 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: | Predicted trans-membrane segments: 1

Druggability Group : DG3

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

PF13091   PLD-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0032049   cardiolipin biosynthetic process  
GO:0016020   membrane  
GO:0008444   CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Metabolic Pathways

Glycerophospholipid metabolism (KEGG)
Global map (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
12 91 3l21 (A) 13 86 39.00 0.57 0.56 0.416681 0.21
79 325 3hsi (A) 19 245 25.00 0.00033 0.9 0.593226 -0.3
85 271 1byr (A) 4 151 19.00 0 0.94 0.300965 -0.1
271 327 1zgr (A) 288 348 30.00 0.96 0.05 0.227283 0.92

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. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_128543)

Species Accession Gene Product
Babesia bovis BBOV_IV011790   phosphatidylglycerophosphate synthase, putative
Brugia malayi Bm1_19760   Phospholipase D. Active site motif family protein
Candida albicans CaO19.7072   phosphatidylglycerolphosphate synthase
Candida albicans CaO19_7072   hypothetical protein
Caenorhabditis elegans CELE_Y48G1C.4   Protein PGS-1
Cryptosporidium hominis Chro.20123   silencer-associated factor
Cryptosporidium parvum cgd2_1110   silencer-associated factor, putative
Dictyostelium discoideum DDB_G0277037   phosphatidylglycerophosphate synthase 1
Drosophila melanogaster Dmel_CG7718   CG7718 gene product from transcript CG7718-RA
Escherichia coli b2585   phosphatidylserine synthase (CDP-diacylglycerol-serine O-phosphatidyltransferase)
Echinococcus granulosus EgrG_000624900   CDP diacylglycerol glycerol 3 phosphate
Echinococcus multilocularis EmuJ_000625250   leukocyte receptor cluster
Echinococcus multilocularis EmuJ_000624900   CDP diacylglycerol glycerol 3 phosphate
Homo sapiens ENSG00000087157   phosphatidylglycerophosphate synthase 1
Leishmania braziliensis LbrM.07.0200   phosphatidylglycerophosphate synthase, putative
Leishmania donovani LdBPK_070360.1   phosphatidylglycerolphosphate synthase, mitochondrial, putative
Leishmania infantum LinJ.07.0360   phosphatidylglycerophosphate synthase, putative
Leishmania major LmjF.07.0200   phosphatidylglycerophosphate synthase, putative
Leishmania mexicana LmxM.07.0200   phosphatidylglycerophosphate synthase-like protein
Loa Loa (eye worm) LOAG_11197   hypothetical protein
Loa Loa (eye worm) LOAG_06803   hypothetical protein
Mus musculus ENSMUSG00000017715   phosphatidylglycerophosphate synthase 1
Plasmodium berghei PBANKA_0710600   phosphatidylglycerophosphate synthase, putative
Plasmodium falciparum PF3D7_0820200   phosphatidylglycerophosphate synthase
Plasmodium knowlesi PKNH_1314000   phosphatidylglycerophosphate synthase, putative
Plasmodium vivax PVX_089355   phosphatidylglycerophosphate synthase, putative
Plasmodium yoelii PY03489   phosphatidylglycerophosphate synthase-related
Saccharomyces cerevisiae YCL004W   CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Schistosoma japonicum Sjp_0027940   ko:K00995 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase [EC2.7.8.5], putative
Schistosoma japonicum Sjp_0027930   ko:K00998 phosphatidylserine synthase [EC2.7.8.8], putative
Schistosoma mansoni Smp_090820   CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Schmidtea mediterranea mk4.002276.01   CDP-diacylglycerolALQ-glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
Trypanosoma brucei gambiense Tbg972.8.1340   phosphatidylglycerophosphate synthase-like protein, putative
Trypanosoma brucei Tb927.8.1720   phosphatidylglycerolphosphate synthase, mitochondrial
Trypanosoma congolense TcIL3000_8_1620   phosphatidylglycerolphosphate synthase, mitochondrial, putative
Trypanosoma cruzi TcCLB.505071.100   phosphatidylglycerolphosphate synthase, mitochondrial, putative
Trypanosoma cruzi TcCLB.511395.20   phosphatidylglycerolphosphate synthase, mitochondrial, putative
Theileria parva TP01_1130   phosphatidylglycerophosphate synthase, putative

Essentiality

Tb927.8.1720 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.1720 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.1720 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.1720 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.1720 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2585 Escherichia coli essential goodall
CELE_Y48G1C.4 Caenorhabditis elegans embryonic lethal wormbase
YCL004W Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • 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
  • 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) 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) 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

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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User comments

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Gene identifier Tb927.8.1720 (Trypanosoma brucei), phosphatidylglycerolphosphate synthase, mitochondrial
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