Detailed view for Tb927.11.4690

Basic information

TDR Targets ID: 12171
Trypanosoma brucei, mitochondrial DNA polymerase I protein B
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.5251 | Length (AA): 1404 | MW (Da): 158715 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

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

PF00476   DNA polymerase family A
PF00929   Exonuclease

Gene Ontology

Mouse over links to read term descriptions.
GO:0016797   exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters  
GO:0005739   mitochondrion  
GO:0005622   intracellular  
GO:0003676   nucleic acid binding  
GO:0004527   exonuclease activity  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003677   DNA binding  
GO:0006261   DNA-dependent DNA replication  
GO:0006260   DNA replication  

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
755 946 3v9w (A) 11 194 20.00 0 1 0.262552 -0.4
759 1358 1kfd (A) 347 921 21.00 0 1 0.46215 0.81
762 951 2gui (A) 7 180 25.00 0 0.95 0.247128 -0.11
763 832 4fzx (C) 2 71 40.00 0 0.63 0.401658 -0.03

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_136918)

Species Accession Gene Product
Arabidopsis thaliana AT5G26940   Mg2+-dependent DNA exonuclease
Chlamydia trachomatis CT_261   DNA polymerase III subunit epsilon
Leishmania braziliensis LbrM.13.0070   mitochondrial DNA polymerase I protein B, putative
Leishmania donovani LdBPK_130080.1   mitochondrial DNA polymerase I protein B, putative
Leishmania infantum LinJ.13.0080   mitochondrial DNA polymerase I protein B, putative
Leishmania major LmjF.13.0080   mitochondrial DNA polymerase I protein B, putative
Leishmania mexicana LmxM.13.0080   mitochondrial DNA polymerase I protein B, putative
Mycobacterium ulcerans MUL_1148   DNA polymerase
Oryza sativa 4332575   Os03g0301400
Trypanosoma brucei gambiense Tbg972.11.5330   hypothetical protein, conserved,mitochondrial DNA polymerase I
Trypanosoma brucei Tb927.11.4690   mitochondrial DNA polymerase I protein B
Trypanosoma congolense TcIL3000.11.4800   mitochondrial DNA polymerase I protein B, putative
Trypanosoma cruzi TcCLB.511847.60   mitochondrial DNA polymerase I protein B, putative
Trypanosoma cruzi TcCLB.506227.80   mitochondrial DNA polymerase I protein B, putative

Essentiality

Tb927.11.4690 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.2300 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.2300 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.2300 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.2300 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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) 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

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
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

22 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 Tb927.11.4690 (Trypanosoma brucei), mitochondrial DNA polymerase I protein B
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