Detailed view for LmjF.03.0090

Basic information

TDR Targets ID: 21603
Leishmania major, DNA primase large subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.4515 | Length (AA): 567 | MW (Da): 63533 | 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

PF04104   Eukaryotic and archaeal DNA primase, large subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0006269   DNA replication, synthesis of RNA primer  
GO:0005658   alpha DNA polymerase:primase complex  
GO:0016779   nucleotidyltransferase activity  
GO:0003896   DNA primase activity  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
DNA replication (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
123 295 1zt2 (B) 29 201 11.00 0.000000026 0.18 0.16 -0.1
28 534 4rr2 (D) 22 456 29.00 0 1 0.99228 0.45
133 289 4rr2 (B) 76 234 22.00 0 0.87 0.491196 0.15
331 533 3lgb (A) 316 511 33.00 0 1 0.676125 -0.75
339 510 5dqo (A) 276 432 47.00 0 1 0.453051 0.41

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_127945)

Species Accession Gene Product
Arabidopsis thaliana AT1G67320   probable DNA primase large subunit
Babesia bovis BBOV_IV002300   DNA primase, large subunit
Brugia malayi Bm1_51365   Eukaryotic-type DNA primase, large subunit family protein
Candida albicans CaO19.10403   DNA primase large subunit
Candida albicans CaO19.2885   DNA primase large subunit
Caenorhabditis elegans CELE_W02D9.1   Protein PRI-2, isoform B
Cryptosporidium hominis Chro.80166   hypothetical protein
Cryptosporidium parvum cgd8_1410   DNA primase large subunit
Dictyostelium discoideum DDB_G0270442   DNA polymerase alpha primase subunit
Drosophila melanogaster Dmel_CG5553   DNA polymerase alpha 60kD
Echinococcus granulosus EgrG_000487100   DNA primase large subunit
Entamoeba histolytica EHI_147530   DNA primase large subunit, putative
Echinococcus multilocularis EmuJ_000487100   DNA primase large subunit
Giardia lamblia GL50803_6980   DNA pol/primase, large sub
Homo sapiens 101930420   DNA primase large subunit-like
Homo sapiens ENSG00000146143   primase, DNA, polypeptide 2 (58kDa)
Leishmania braziliensis LbrM.03.0100   DNA primase large subunit, putative
Leishmania donovani LdBPK_030080.1   DNA primase large subunit, putative
Leishmania infantum LinJ.03.0080   DNA primase large subunit, putative
Leishmania major LmjF.03.0090   DNA primase large subunit, putative
Leishmania mexicana LmxM.03.0090   DNA primase large subunit, putative
Loa Loa (eye worm) LOAG_07121   hypothetical protein
Loa Loa (eye worm) LOAG_12771   hypothetical protein
Mus musculus ENSMUSG00000026134   DNA primase, p58 subunit
Neospora caninum NCLIV_006750   DNA primase, large subunit, putative
Oryza sativa 4342990   Os07g0406800
Plasmodium berghei PBANKA_0812000   DNA primase large subunit, putative
Plasmodium falciparum PF3D7_0910900   DNA primase large subunit, putative
Plasmodium knowlesi PKNH_0708900   DNA primase large subunit, putative
Plasmodium vivax PVX_098985   DNA primase large subunit, putative
Plasmodium yoelii PY00851   DNA primase large subunit
Saccharomyces cerevisiae YKL045W   DNA primase subunit PRI2
Schistosoma japonicum Sjp_0022440   ko:K02685 DNA primase large subunit, putative
Schistosoma japonicum Sjp_0132960   ko:K02685 DNA primase large subunit, putative
Schistosoma mansoni Smp_079050.1   DNA primase large subunit
Schmidtea mediterranea mk4.004339.00   DNA primase large subunit
Schmidtea mediterranea mk4.012252.05  
Schmidtea mediterranea mk4.012252.03   DNA primase large subunit
Schmidtea mediterranea mk4.011200.00   DNA primase large subunit
Schmidtea mediterranea mk4.012252.02   DNA primase large subunit
Schmidtea mediterranea mk4.034123.00   DNA primase large subunit
Schmidtea mediterranea mk4.044580.00   DNA primase large subunit
Schmidtea mediterranea mk4.019229.01   DNA primase large subunit
Schmidtea mediterranea mk4.006282.00   DNA primase large subunit
Trypanosoma brucei gambiense Tbg972.10.3940   DNA primase large subunit, putative
Trypanosoma brucei Tb927.10.3110   DNA primase large subunit, putative
Trypanosoma cruzi TcCLB.510943.140   DNA primase large subunit, putative
Trypanosoma cruzi TcCLB.504867.80   DNA primase large subunit, putative
Toxoplasma gondii TGME49_297840   DNA primase, large subunit
Theileria parva TP03_0424   DNA primase large subunit, putative
Trichomonas vaginalis TVAG_091480   DNA primase large subunit, putative

Essentiality

LmjF.03.0090 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3110 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.3110 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.3110 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.3110 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_W02D9.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_W02D9.1 Caenorhabditis elegans sterile wormbase
YKL045W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0812000 Plasmodium berghei Essential plasmo
TGME49_297840 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.
  • 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.
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier LmjF.03.0090 (Leishmania major), DNA primase large subunit, putative
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