Detailed view for LdBPK_281540.1

Basic information

TDR Targets ID: 817983
Leishmania donovani, DNA polymerase kappa, putative
Source Database / ID: 

pI: 8.0099 | Length (AA): 598 | MW (Da): 67050 | Paralog Number: 1

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

PF00817   impB/mucB/samB family
PF11799   impB/mucB/samB family C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003684   damaged DNA binding  
GO:0006281   DNA repair  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
29 135 4tql (A) 64 164 17.00 0.55 0.01 0.23123 -0.16
61 483 2oh2 (B) 22 516 36.00 0 1 1.10626 -0.18
121 487 3gqc (A) 365 828 26.00 0 1 0.775612 0.24
143 480 5c5j (F) 2 336 31.00 0 1 0.913117 0.15
143 376 4dez (A) 3 237 28.00 0.0000015 1 0.744604 -0.18

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_127393)

Species Accession Gene Product
Arabidopsis thaliana AT1G49980   DNA/RNA polymerases superfamily protein
Brugia malayi Bm1_37790   polk-prov protein
Caenorhabditis elegans CELE_F22B7.6   Protein POLK-1, isoform B
Dictyostelium discoideum DDB_G0287149   UMUC-like DNA-repair protein
Escherichia coli b0231   DNA polymerase IV
Echinococcus granulosus EgrG_000832500   dna polymerase kappa
Echinococcus multilocularis EmuJ_000832500   dna polymerase kappa
Giardia lamblia GL50803_16810   DINP protein human, muc B family
Homo sapiens ENSG00000122008   polymerase (DNA directed) kappa
Leishmania braziliensis LbrM.28.1580   DNA polymerase kappa, putative,DNA polymerase IV, putative
Leishmania braziliensis LbrM.28.1570   DNA polymerase kappa, putative
Leishmania donovani LdBPK_281540.1   DNA polymerase kappa, putative
Leishmania donovani LdBPK_281530.1   DNA polymerase kappa, putative
Leishmania infantum LinJ.28.1530   DNA polymerase kappa, putative
Leishmania infantum LinJ.28.1540   DNA polymerase kappa, putative,DNA polymerase IV, putative
Leishmania major LmjF.28.1420   DNA polymerase kappa, putative,DNA polymerase IV, putative
Leishmania major LmjF.28.1410   DNA polymerase kappa, putative
Leishmania mexicana LmxM.28.1410   DNA polymerase kappa, putative
Leishmania mexicana LmxM.28.1420   DNA polymerase kappa, putative,DNA polymerase IV, putative
Loa Loa (eye worm) LOAG_02290   hypothetical protein
Mus musculus ENSMUSG00000021668   polymerase (DNA directed), kappa
Mycobacterium tuberculosis Rv1537   Probable DNA polymerase IV DinX (pol IV 1) (DNA nucleotidyltransferase (DNA-directed))
Mycobacterium tuberculosis Rv3056   Possible DNA-damage-inducible protein P DinP (DNA polymerase V) (pol IV 2) (DNA nucleotidyltransferase (DNA-directed))
Mycobacterium ulcerans MUL_1535   DNA polymerase IV
Mycobacterium ulcerans MUL_5028   DNA polymerase IV
Oryza sativa 4333450   Os03g0616300
Schistosoma japonicum Sjp_0121940   ko:K03511 DNA polymerase kappa subunit, putative
Schmidtea mediterranea mk4.024598.01  
Schmidtea mediterranea mk4.025253.00  
Schmidtea mediterranea mk4.036851.03   DNA polymerase iota
Schmidtea mediterranea mk4.002814.01   DNA polymerase kappa
Schmidtea mediterranea mk4.014952.00  
Schmidtea mediterranea mk4.001540.00  
Schmidtea mediterranea mk4.002814.00  
Trypanosoma brucei gambiense Tbg972.11.9710   DNA polymerase kappa, putative
Trypanosoma brucei gambiense Tbg972.11.9680   DNA polymerase kappa, putative
Trypanosoma brucei gambiense Tbg972.11.9700   DNA polymerase kappa, putative
Trypanosoma brucei gambiense Tbg972.11.9720   DNA polymerase kappa, putative,DNA polymerase IV, putative
Trypanosoma brucei gambiense Tbg972.11.9690   DNA polymerase kappa, putative
Trypanosoma brucei gambiense Tbg972.11.9670   DNA polymerase kappa, putative,DNA polymerase IV, putative
Trypanosoma brucei gambiense Tbg972.11.9660   DNA polymerase kappa, putative,DNA polymerase IV, putative
Trypanosoma brucei Tb11.v5.0764   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.1050   DNA polymerase kappa, putative
Trypanosoma brucei Tb927.11.8490   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.0661   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.0526   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.0711   DNA polymerase kappa, putative
Trypanosoma brucei Tb927.11.8510   DNA polymerase kappa, putative
Trypanosoma brucei Tb927.11.8480   DNA polymerase kappa, putative
Trypanosoma brucei Tb427tmp.01.0010   DNA polymerase IV, putative
Trypanosoma brucei Tb927.11.8680   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.0756   DNA polymerase kappa, putative
Trypanosoma brucei Tb427tmp.01.0030   DNA polymerase IV, putative
Trypanosoma brucei Tb11.v5.0878   DNA polymerase kappa, putative
Trypanosoma brucei Tb927.11.8500   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.1058   DNA polymerase kappa, putative
Trypanosoma brucei Tb11.v5.1056   DNA polymerase kappa, putative
Trypanosoma brucei Tb927.11.8520   DNA polymerase kappa, putative
Trypanosoma congolense TcIL3000_0_59930   DNA polymerase kappa, putative
Trypanosoma cruzi TcCLB.503755.30   DNA polymerase kappa, putative
Trypanosoma cruzi TcCLB.503755.10   DNA polymerase kappa, putative
Trypanosoma cruzi TcCLB.510131.70   DNA polymerase kappa, putative
Trypanosoma cruzi TcCLB.510131.50   DNA polymerase kappa, putative
Toxoplasma gondii TGME49_237480   BRCA1 C Terminus (BRCT) domain-containing protein
Trichomonas vaginalis TVAG_062670   DNA polymerase IV / kappa, putative
Trichomonas vaginalis TVAG_177420   DNA polymerase eta, putative

Essentiality

LdBPK_281540.1 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3109 Mycobacterium tuberculosis non-essential nmpdr
Tb11.12.0001 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.12.0001 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.12.0001 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.12.0001 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.12.0019 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.12.0019 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.12.0019 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.12.0019 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.01.0010 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.0010 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.0010 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.0010 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0231 Escherichia coli non-essential goodall
TGME49_237480 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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.
  • 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

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
Homo sapiens polymerase (DNA directed) kappa 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_281540.1 (Leishmania donovani), DNA polymerase kappa, putative
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