Detailed view for LdBPK_080830.1

Basic information

TDR Targets ID: 817933
Leishmania donovani, mitochondrial DNA polymerase beta
Source Database / ID: 

pI: 9.3822 | Length (AA): 376 | MW (Da): 42673 | Paralog Number: 0

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

Druggability Group : DG

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

PF10391   Fingers domain of DNA polymerase lambda
PF14716   Helix-hairpin-helix domain
PF14791   DNA polymerase beta thumb
PF14792   DNA polymerase beta palm

Gene Ontology

Mouse over links to read term descriptions.
GO:0034061   DNA polymerase activity  
GO:0005634   nucleus  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003677   DNA binding  
GO:0006281   DNA repair  

Metabolic Pathways

Base excision repair (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
10 80 2kp7 (A) 16 84 19.00 0 0.96 0.56593 -1.45
20 376 4p4o (A) 20 376 99.99 0 1 1.90357 -0.23

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_130965)

Species Accession Gene Product
Dictyostelium discoideum DDB_G0284713   DNA polymerase X family protein
Homo sapiens ENSG00000070501   polymerase (DNA directed), beta
Leishmania braziliensis LbrM.08.0710   mitochondrial DNA polymerase beta
Leishmania donovani LdBPK_080830.1   mitochondrial DNA polymerase beta
Leishmania infantum LinJ.08.0830   mitochondrial DNA polymerase beta
Leishmania major LmjF.08.0890   mitochondrial DNA polymerase beta
Leishmania mexicana LmxM.08.0890   mitochondrial DNA polymerase beta
Mus musculus ENSMUSG00000031536   polymerase (DNA directed), beta
Mycobacterium tuberculosis Rv3856c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_5029   hypothetical protein
Trypanosoma brucei gambiense Tbg972.5.3920   mitochondrial DNA polymerase beta
Trypanosoma brucei Tb927.5.2780   mitochondrial DNA polymerase beta
Trypanosoma congolense TcIL3000_5_2920   mitochondrial DNA polymerase beta, putative
Trypanosoma cruzi TcCLB.503955.20   mitochondrial DNA polymerase beta, putative
Trypanosoma cruzi TcCLB.507063.90   mitochondrial DNA polymerase beta, putative

Essentiality

LdBPK_080830.1 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3923 Mycobacterium tuberculosis non-essential nmpdr
Tb927.5.2780 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.2780 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.5.2780 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.5.2780 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.
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

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
Species Known druggable target Linked compounds Reference
Mus musculus polymerase (DNA directed), beta Compounds References
Homo sapiens polymerase (DNA directed), beta Compounds References
Rattus norvegicus DNA polymerase beta Compounds References
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

No literature references available for this target.

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

User comments

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Gene identifier LdBPK_080830.1 (Leishmania donovani), mitochondrial DNA polymerase beta
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