Detailed view for LmjF.33.1690

Basic information

TDR Targets ID: 23180
Leishmania major, DNA polymerase delta catalytic subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.6214 | Length (AA): 1032 | MW (Da): 116619 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00136   DNA polymerase family B
PF03104   DNA polymerase family B, exonuclease domain
PF14260   C4-type zinc-finger of DNA polymerase delta

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0000166   nucleotide binding  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0006260   DNA replication  

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
1 919 2gv9 (A) 115 1193 26.00 0 1 0.99 -0.25
9 891 2gv9 (A) 123 1166 28.00 0 1 1.07 -0.24
250 922 1tgo (A) 124 767 32.00 0 1 0.99 -0.43
7 906 3iay (A) 95 977 48.00 0 1 1.40499 -0.31
28 1012 5exr (C) 343 1377 22.00 0 1 0.978057 1.3

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, 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_127429)

Species Accession Gene Product
Arabidopsis thaliana AT5G63960   DNA polymerase delta subunit 1
Babesia bovis BBOV_IV008750   DNA polymerase delta subunit
Brugia malayi Bm1_06910   DNA polymerase delta catalytic subunit
Candida albicans CaO19.5182   N terminus of DNA-directed DNA polymerase III (delta)
Candida albicans CaO19.12649   N terminus of DNA-directed DNA polymerase III (delta)
Candida albicans CaO19_5182   hypothetical protein
Caenorhabditis elegans CELE_F10C2.4   Protein F10C2.4
Cryptosporidium hominis Chro.60506   DNA polymerase family B subunit
Cryptosporidium parvum cgd6_4410   DNA polymerase delta catalytic subunit. DNAQ-like 3-5 exonuclease; RNAseH fold
Dictyostelium discoideum DDB_G0285381   DNA polymerase delta catalytic subunit
Drosophila melanogaster Dmel_CG5949   DNA-polymerase-delta
Escherichia coli b0060   DNA polymerase II
Echinococcus granulosus EgrG_000795600   DNA polymerase delta catalytic subunit
Entamoeba histolytica EHI_006690   DNA polymerase delta catalytic subunit, putative
Echinococcus multilocularis EmuJ_000795600   DNA polymerase delta catalytic subunit
Giardia lamblia GL50803_35094   DNA polymerase delta, catalytic subunit
Homo sapiens ENSG00000062822   polymerase (DNA directed), delta 1, catalytic subunit
Leishmania braziliensis LbrM.33.1960   DNA polymerase delta catalytic subunit, putative
Leishmania donovani LdBPK_331790.1   DNA polymerase delta catalytic subunit, putative
Leishmania infantum LinJ.33.1790   DNA polymerase delta catalytic subunit, putative
Leishmania major LmjF.33.1690   DNA polymerase delta catalytic subunit, putative
Leishmania mexicana LmxM.32.1690   DNA polymerase delta catalytic subunit, putative
Loa Loa (eye worm) LOAG_07617   DNA-directed DNA polymerase III
Mus musculus ENSMUSG00000038644   polymerase (DNA directed), delta 1, catalytic subunit
Neospora caninum NCLIV_028330   DNA polymerase (EC 2.7.7.7), related
Oryza sativa 4349968   Os11g0186400
Onchocerca volvulus OVOC1223   DNA polymerase delta catalytic subunit homolog
Plasmodium berghei PBANKA_0501300   DNA polymerase delta catalytic subunit, putative
Plasmodium falciparum PF3D7_1017000   DNA polymerase delta catalytic subunit
Plasmodium knowlesi PKNH_0601200   DNA polymerase delta catalytic subunit, putative
Plasmodium vivax PVX_001720   DNA polymerase delta catalytic subunit, putative
Plasmodium yoelii PY00203   DNA polymerase delta catalytic subunit
Saccharomyces cerevisiae YDL102W   DNA-directed DNA polymerase delta POL3
Schistosoma japonicum Sjp_0046040   ko:K02327 DNA polymerase delta subunit 1, putative
Schistosoma mansoni Smp_087010   DNA polymerase delta catalytic subunit
Schmidtea mediterranea mk4.001650.03  
Schmidtea mediterranea mk4.001650.02  
Schmidtea mediterranea mk4.003004.01   DNA polymerase delta catalytic subunit
Schmidtea mediterranea mk4.023618.00   DNA polymerase delta catalytic subunit
Trypanosoma brucei gambiense Tbg.972.2.350   DNA polymerase delta catalytic subunit, putative
Trypanosoma brucei Tb927.2.1800   DNA polymerase delta catalytic subunit, putative
Trypanosoma congolense TcIL3000_2_40   DNA polymerase delta catalytic subunit, putative
Trypanosoma cruzi TcCLB.509215.10   DNA polymerase delta catalytic subunit, putative
Trypanosoma cruzi TcCLB.507265.30   DNA polymerase delta catalytic subunit, putative
Toxoplasma gondii TGME49_258030   DNA polymerase
Theileria parva TP01_0899   DNA polymerase delta catalytic subunit, putative
Trichomonas vaginalis TVAG_038580   DNA polymerase zeta catalytic subunit, putative

Essentiality

LmjF.33.1690 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.1800 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.2.1800 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.2.1800 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.2.1800 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0060 Escherichia coli non-essential goodall
CELE_F10C2.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_F10C2.4 Caenorhabditis elegans larval lethal wormbase
YDL102W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0501300 Plasmodium berghei Essential plasmo
TGME49_258030 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • 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
  • 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

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

Druggability index (range: 0 to 1): 0.8

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
Human herpesvirus 6A (strain Uganda-1102) (HHV-6 variant A) (Human Blymphotropic virus) Human herpesvirus 6 DNA polymerase Compounds References
Human herpesvirus 1 (strain KOS) (HHV-1) (Human herpes simplex virus1) DNA polymerase catalytic subunit Compounds References
Human cytomegalovirus (strain AD169) (HHV-5) (Human herpesvirus 5) Human herpesvirus 5 DNA polymerase Compounds References
Homo sapiens polymerase (DNA directed), delta 1, catalytic subunit Compounds References
Herpes simplex virus (type 1 / strain 17) Human herpesvirus 1 DNA polymerase Compounds References
Varicella-zoster virus (strain Dumas) (HHV-3) (Human herpesvirus 3) DNA polymerase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.1749 0.5244 1
0.0278 0.2692 0.8919
0.0356 0.5122 1
0.0269 0.4983 0.8532
0.0253 1 1
0.0154 0.4453 1
0.1013 1 1
0.2006 1 1
0.1546 0.2889 1
0.0092 0.5396 1
0.0152 0.3399 1
0.1034 1 1
0.0092 0.4808 1
0.0615 1 1
0.0076 0.3494 0.3494
0.2594 1 1
0.0082 0.379 0.379
0.0157 0.4217 1
0.0075 0.3754 1
0.0276 0.5433 0.8746
0.1048 1 1
0.0075 0.3189 0.3189
0.0074 1 1
0.0256 0.2547 0.6673
0.0146 1 1
0.2002 1 1
0.0092 1 0.5
0.0323 0.2864 0.4011
0.0076 0.3317 0.3317
0.0413 1 1
0.0296 0.3278 0.3625
0.1406 1 1
0.0245 0.3327 1
0.0361 0.5119 1
0.1681 0.827 1
0.0336 0.5939 1
0.0023 1 0.5
0.0241 0.336 1
0.0342 0.6532 1
0.008 0.7032 0.6441
0.1669 1 1
0.0075 1 1
0.0074 0.329 0.329
0.0361 0.5104 1
0.0361 0.5107 1
0.0892 1 1
0.0266 0.544 0.8628
0.0342 0.5631 1
0.0336 0.5939 1
0.0322 1 1
0.0361 0.4528 1
0.105 1 1
0.0631 0.6886 1
0.0278 0.4472 0.8746
0.0385 0.6634 1
0.0364 0.5123 0.8361
0.024 0.5389 1
0.2248 1 1
0.1546 0.2889 1
0.0225 0.2811 1
0.0159 1 1
0.0253 0.6236 1
0.0206 0.685 1
0.0123 1 1
0.0361 0.4112 1
0.0636 1 1
0.0691 1 1
0.008 0.2969 0.2969
0.027 0.3166 0.4077
0.0278 0.2692 0.8919
0.011 0.2541 1
0.0076 0.3322 0.3322
0.0267 0.5438 0.8821
0.2594 1 1
0.1579 1 1
0.0392 0.7377 0.7338
0.024 0.2872 1
0.0382 0.4642 1
0.0265 0.5454 0.8634
0.2424 1 1
0.0856 1 1
0.0074 0.6749 0.9816
0.0075 0.3324 0.3324
0.248 1 1
0.0346 0.4583 1
0.296 0.3497 1
0.0074 1 1
0.027 0.878 0.8511
0.0154 1 1
0.0413 1 1
0.0315 0.3665 0.8684
0.2005 1 1
0.0412 1 1
0.1244 1 1
0.0612 1 1
0.0466 1 1
0.0407 0.4374 1
0.0074 0.4617 1
0.0076 0.3123 0.612
0.0224 0.6641 0.8712
0.0303 0.5019 0.8735
0.0345 1 1
0.0092 1 0.5
0.0159 0.3394 1
0.0361 0.5107 1
0.0074 0.3809 1
0.0279 0.7258 0.8686
0.0631 0.6886 1
0.0385 0.4361 1
0.1433 1 1
0.0326 0.2956 0.8821
0.0115 1 1
0.0075 1 1
0.0078 0.4251 0.4251
0.0361 0.5123 1
0.0336 0.3055 0.4722
0.0076 0.2749 1
0.2258 0.4327 1
0.0074 1 1
0.0361 0.5064 1
0.0382 0.5118 1
0.0152 0.5812 1
0.0042 1 1
0.0405 0.3998 1
0.0123 1 1
0.0075 1 1
0.0078 0.4132 0.4468
0.0074 0.5359 1
0.1036 0.6113 1
0.0387 0.4157 1
0.0361 0.8644 1
0.0504 0.5375 1
0.0361 0.5841 1
0.0382 0.4633 1
0.0336 0.3055 0.4722
0.0264 0.4036 0.8511
0.181 1 1
0.0356 0.5826 1
0.1433 1 1
0.2594 1 1
0.0263 0.5309 0.8651
0.0282 0.4559 0.8689
0.2258 0.4327 1
0.0336 0.3055 0.4722
0.2413 1 1
0.1494 0.6752 1
0.008 0.2969 0.2969
0.0078 0.4251 0.4251
0.027 0.878 0.8511
0.0703 0.3743 1
0.0075 0.3635 0.6113
0.2594 1 1
0.0075 0.3289 0.3289
0.2248 1 1
0.1749 0.5244 1
0.0361 0.5955 1
0.1013 1 1
0.248 1 1
0.0253 1 1
0.0075 0.3811 1
0.0355 0.7933 1
0.0079 0.3861 1
0.0075 0.3076 0.272
0.0364 0.3909 1
0.023 0.7536 1
0.2258 0.4327 1
0.0078 0.3389 0.3382
0.1433 1 1
0.0074 0.9471 0.9401
0.027 0.878 0.8511
0.0353 0.4706 1
0.0077 0.3339 0.3339
0.0361 0.4128 1
0.0382 0.5118 1
0.0344 1 1
0.1669 1 1
0.0364 0.5123 0.8361
0.0075 0.3295 0.3295
0.0658 1 1
0.0077 0.3339 0.3339
0.0075 0.2719 1
0.0282 0.3854 0.8749
0.0213 1 1
0.0085 0.4211 0.478
0.0253 1 1
0.0336 0.3055 0.4722
0.0481 1 1
0.0407 0.5754 1
0.0322 0.5819 1
0.0481 1 1
0.0083 0.3919 0.4462
0.0675 0.7986 1
0.0336 0.9061 0.8873
0.0153 0.5158 0

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.33.1690 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.

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Gene identifier LmjF.33.1690 (Leishmania major), DNA polymerase delta catalytic subunit, putative
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