Detailed view for LmjF.35.1790

Basic information

TDR Targets ID: 29684
Leishmania major, DNA polymerase epsilon subunit b, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.2715 | Length (AA): 552 | MW (Da): 61376 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF04042   DNA polymerase alpha/epsilon subunit B

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
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 3 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
2 75 2v6z (M) 28 99 11.00 0.000007 0.13 0.406958 -1.81
105 537 5ihe (A) 194 587 18.00 0 1 0.75232 0.71
252 543 4y97 (A) 317 578 17.00 0 1 0.547585 0.33

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
Mid 40-60% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_128285)

Species Accession Gene Product
Arabidopsis thaliana AT5G22110   DNA polymerase epsilon subunit B2
Brugia malayi Bm1_34750   DNA polymerase epsilon subunit B
Brugia malayi Bm1_34755   pole2 protein
Candida albicans CaO19.7564   similar to S. cerevisiae DPB2 (YPR175W) DNA polymerase epsilon subunit B
Caenorhabditis elegans CELE_F08B4.5   Protein POLE-2
Cryptosporidium hominis Chro.20265   hypothetical protein
Cryptosporidium parvum cgd2_2500   DNA polymerase epsilon subunit
Dictyostelium discoideum DDB_G0278367   hypothetical protein
Drosophila melanogaster Dmel_CG10489   CG10489 gene product from transcript CG10489-RA
Echinococcus granulosus EgrG_000414300   dna polymerase epsilon subunit 2
Echinococcus multilocularis EmuJ_000414300   dna polymerase epsilon subunit 2
Giardia lamblia GL50803_3706   DNA pol epsilon, sub B
Homo sapiens ENSG00000100479   polymerase (DNA directed), epsilon 2, accessory subunit
Leishmania braziliensis LbrM.34.1700   DNA polymerase epsilon subunit b, putative
Leishmania donovani LdBPK_351780.1   DNA polymerase epsilon subunit B, putative
Leishmania infantum LinJ.35.1780   DNA polymerase epsilon subunit b, putative
Leishmania major LmjF.35.1790   DNA polymerase epsilon subunit b, putative
Leishmania mexicana LmxM.34.1790   DNA polymerase epsilon subunit b, putative
Loa Loa (eye worm) LOAG_01229   pole2 protein
Loa Loa (eye worm) LOAG_14095   hypothetical protein
Loa Loa (eye worm) LOAG_08035   hypothetical protein
Mus musculus ENSMUSG00000020974   polymerase (DNA directed), epsilon 2 (p59 subunit)
Oryza sativa 9272695   Os08g0466050
Oryza sativa 4337886   Os05g0160800
Onchocerca volvulus OVOC7346   Putative DNA polymerase epsilon subunit 2
Onchocerca volvulus OVOC7341   Putative DNA polymerase epsilon subunit 2
Plasmodium berghei PBANKA_1448900   DNA polymerase epsilon subunit B, putative
Plasmodium falciparum PF3D7_1234300   DNA polymerase epsilon subunit B, putative
Plasmodium knowlesi PKNH_1453700   DNA polymerase epsilon subunit B, putative
Plasmodium vivax PVX_100665   hypothetical protein, conserved
Plasmodium yoelii PY06200   DNA polymerase epsilon subunit b
Saccharomyces cerevisiae YPR175W   Dpb2p
Schistosoma japonicum Sjp_0093770   Conserved hypothetical protein
Schistosoma japonicum Sjp_0117470   ko:K02325 DNA polymerase epsilon subunit 2, putative
Schistosoma japonicum Sjp_0000260   ko:K02325 DNA polymerase epsilon subunit 2, putative
Schistosoma mansoni Smp_124120   DNA polymerase epsilon subunit B
Schmidtea mediterranea mk4.000001.39  
Schmidtea mediterranea mk4.003825.00   Putative DNA polymerase epsilon subunit b
Schmidtea mediterranea mk4.005025.01   Putative DNA polymerase epsilon subunit b
Trypanosoma brucei gambiense Tbg972.9.9290   DNA polymerase epsilon subunit b, putative
Trypanosoma brucei Tb927.9.15030   DNA polymerase epsilon subunit B, putative
Trypanosoma congolense TcIL3000_9_6250   DNA polymerase epsilon subunit B, putative
Trypanosoma cruzi TcCLB.509671.160   DNA polymerase epsilon subunit B, putative
Trypanosoma cruzi TcCLB.510763.80   DNA polymerase epsilon subunit B, putative
Trichomonas vaginalis TVAG_030780   DNA polymerase epsilon subunit B, putative

Essentiality

LmjF.35.1790 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.244.2820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.244.2820 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.244.2820 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.244.2820 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F08B4.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F08B4.5 Caenorhabditis elegans larval arrest wormbase
CELE_F08B4.5 Caenorhabditis elegans sterile wormbase
YPR175W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1448900 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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
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

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Leishmania mexicana ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    LmjF.35.1790 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania mexicana ( 1 )

Bibliographic References

9 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.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.35.1790 (Leishmania major), DNA polymerase epsilon subunit b, putative
Title for this comment
Comment