Detailed view for Tb11.v5.0667

Basic information

TDR Targets ID: 15141
Trypanosoma brucei, poly(A) polymerase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.5366 | Length (AA): 333 | MW (Da): 37669 | Paralog Number: 0

Signal peptide: N | 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

PF03828   Cid1 family poly A polymerase

Gene Ontology

Mouse over links to read term descriptions.
GO:0003674   molecular_function  
GO:0008150   biological_process  
GO:0005739   mitochondrion  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 2 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
1 333 2nom (B) 1 333 99.99 0 1 1.7997 -0.05
3 333 2ikf (A) 3 333 99.99 0 1 2.24069 -1.62

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
  • 2IKF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2NOM:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2Q0C:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2Q0D:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2Q0E:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2Q0F:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2Q0G:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5HZD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5I49:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5IDO:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5KAL:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
NA% 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_128508)

Species Accession Gene Product
Arabidopsis thaliana AT2G45620   Nucleotidyltransferase family protein
Babesia bovis BBOV_IV006780   conserved hypothetical protein
Brugia malayi Bm1_45545   PAP/25A associated domain containing protein
Caenorhabditis elegans CELE_K10D2.3   Protein CID-1
Caenorhabditis elegans CELE_K10D2.2   Protein PUP-2
Dictyostelium discoideum DDB_G0278425   hypothetical protein
Echinococcus granulosus EgrG_001047900   terminal uridylyltransferase 7
Entamoeba histolytica EHI_092480   poly(A) polymerase, putative
Entamoeba histolytica EHI_170350   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001047900   terminal uridylyltransferase 7
Homo sapiens ENSG00000083223   zinc finger, CCHC domain containing 6
Homo sapiens ENSG00000134744   zinc finger, CCHC domain containing 11
Leishmania braziliensis LbrM.32.2690   hypothetical protein, conserved
Leishmania donovani LdBPK_322600.1   Cid1 family poly A polymerase, putative
Leishmania infantum LinJ.32.2600   hypothetical protein, conserved
Leishmania major LmjF.32.2450   hypothetical protein, conserved
Leishmania mexicana LmxM.31.2450   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03356   hypothetical protein
Loa Loa (eye worm) LOAG_01474   hypothetical protein
Mus musculus ENSMUSG00000034610   zinc finger, CCHC domain containing 11
Mus musculus ENSMUSG00000035248   zinc finger, CCHC domain containing 6
Neospora caninum NCLIV_023340   Novel protein (Zgc:110560), related
Oryza sativa 4348226   Os10g0188300
Oryza sativa 9267985   Os02g0122100
Plasmodium berghei PBANKA_1213900   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1015500   conserved Plasmodium protein, unknown function
Plasmodium knowlesi PKNH_0815600   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_094995   hypothetical protein, conserved
Plasmodium yoelii PY04615   caffeine-induced death protein 1
Schmidtea mediterranea mk4.000100.22   Putative zinc finger protein
Schmidtea mediterranea mk4.000100.13   Putative zinc finger protein
Schmidtea mediterranea mk4.000100.06   Putative zinc finger protein
Schmidtea mediterranea mk4.000100.15   Putative zinc finger protein
Schmidtea mediterranea mk4.001365.07   Putative zinc finger protein
Trypanosoma brucei gambiense Tbg972.11.17560   poly(A) polymerase, putative
Trypanosoma brucei Tb11.v5.0667   poly(A) polymerase, putative
Trypanosoma congolense TcIL3000.11.15680   poly(A) polymerase, putative
Trypanosoma cruzi TcCLB.506821.90   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510939.9   hypothetical protein, conserved
Toxoplasma gondii TGME49_281370   polynucleotide adenylyltransferase
Theileria parva TP04_0065   hypothetical protein, conserved

Essentiality

Tb11.v5.0667 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.7300 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.7300 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.7300 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.7300 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_K10D2.2 Caenorhabditis elegans slow growth wormbase
TGME49_281370 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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

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

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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Tb11.v5.0667 (Trypanosoma brucei), poly(A) polymerase, putative
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