Detailed view for PF3D7_1332400

Basic information

TDR Targets ID: 81
Plasmodium falciparum, nucleotidyltransferase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.2852 | Length (AA): 858 | MW (Da): 102029 | 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

PF01909   Nucleotidyltransferase domain
PF03828   Cid1 family poly A polymerase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016779   nucleotidyltransferase activity  

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 8 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
416 711 1q79 (A) 34 358 18.00 0 1 0.21 -1.01
421 767 1fa0 (A) 19 412 18.00 0 1 0.5 -0.75
7 155 4tql (A) 45 195 13.00 0.11 0.01 0.38416 -1.06
409 704 3nyb (A) 161 461 29.00 0.000000000055 1 0.757288 -0.44
441 633 4zrl (A) 561 796 30.00 0.0044 0.95 0.365842 0.57
7 155 4tql (A) 45 195 13.00 0.088 0.01 0.38376 -1.05
12 172 2ap3 (A) 29 194 17.00 0.78 0.06 0.423746 -0.96
409 704 3nyb (A) 161 461 29.00 0.0000000000055 1 0.766888 -0.54

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
Upper 80-100% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, sporozoite, early ring, late ring. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, early schizont, early trophozoite, late trophozoite, Oocyst, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile merozoite, late schizont, Sporozoite, Female Gametocyte, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_127416)

Species Accession Gene Product
Arabidopsis thaliana AT5G53770   nucleotidyltransferase family protein
Babesia bovis BBOV_III006620   hypothetical protein
Brugia malayi Bm1_48580   PAP/25A associated domain containing protein
Candida albicans CaO19.8059   Mitotic chromosome condensation
Candida albicans CaO19.429   Mitotic chromosome condensation
Caenorhabditis elegans CELE_ZK858.1   Protein GLD-4
Cryptosporidium hominis Chro.70404   hypothetical protein
Cryptosporidium parvum cgd7_3630   TRF4/5 nucletotidyl transferase
Dictyostelium discoideum DDB_G0295737   PAP/25A-associated domain-containing protein
Drosophila melanogaster Dmel_CG11265   CG11265 gene product from transcript CG11265-RE
Echinococcus granulosus EgrG_000623000   nucleotidyltransferase
Entamoeba histolytica EHI_087330   topoisomerase, putative
Entamoeba histolytica EHI_003910   hypothetical protein, conserved
Entamoeba histolytica EHI_073170   topoisomerase, putative
Echinococcus multilocularis EmuJ_000623000   nucleotidyltransferase
Giardia lamblia GL50803_16285   Topoisomerase I-related protein
Homo sapiens ENSG00000121274   PAP associated domain containing 5
Homo sapiens ENSG00000112941   PAP associated domain containing 7
Leishmania braziliensis LbrM.07.0770   topoisomerase-related function protein-like protein
Leishmania donovani LdBPK_070780.1   topoisomerase-related function protein-like protein
Leishmania infantum LinJ.07.0780   topoisomerase-related function protein-like protein
Leishmania major LmjF.07.0700   topoisomerase-related function protein-like protein
Leishmania mexicana LmxM.07.0700   topoisomerase-related function protein-like protein
Loa Loa (eye worm) LOAG_05671   PAP/25A associated domain-containing protein
Mus musculus ENSMUSG00000034575   PAP associated domain containing 7
Mus musculus ENSMUSG00000036779   PAP associated domain containing 5
Neospora caninum NCLIV_043710   hypothetical protein, conserved
Oryza sativa 4325901   Os01g0672700
Plasmodium berghei PBANKA_1347200   nucleotidyltransferase, putative
Plasmodium falciparum PF3D7_1332400   nucleotidyltransferase, putative
Plasmodium knowlesi PKNH_1268200   nucleotidyltransferase, putative
Plasmodium vivax PVX_082550   hypothetical protein, conserved
Plasmodium yoelii PY05727   topoisomerase-related function protein
Saccharomyces cerevisiae YOL115W   non-canonical poly(A) polymerase PAP2
Saccharomyces cerevisiae YNL299W   non-canonical poly(A) polymerase TRF5
Schistosoma japonicum Sjp_0133600   ko:K03514 DNA polymerase sigma subunit, putative
Schistosoma japonicum Sjp_0309770   expressed protein
Schistosoma mansoni Smp_145600   hypothetical protein
Schmidtea mediterranea mk4.002515.01  
Schmidtea mediterranea mk4.005006.01  
Schmidtea mediterranea mk4.005006.00  
Trypanosoma brucei gambiense Tbg972.8.650   DNA polymerase sigma, putative
Trypanosoma brucei Tb927.8.1090   NPAPL
Trypanosoma congolense TcIL3000_8_690   DNA polymerase sigma, putative
Trypanosoma cruzi TcCLB.508543.10   DNA polymerase sigma, putative
Trypanosoma cruzi TcCLB.506401.100   DNA polymerase sigma, putative
Toxoplasma gondii TGME49_210440   polynucleotide adenylyltransferase
Theileria parva TP02_0312   hypothetical protein
Trichomonas vaginalis TVAG_080950   Poly(A) RNA polymerase protein, putative
Trichomonas vaginalis TVAG_314620   trf5, putative
Trichomonas vaginalis TVAG_490130   PAP-associated domain-containing protein, putative

Essentiality

PF3D7_1332400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.1090 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.1090 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.1090 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.1090 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK858.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK858.1 Caenorhabditis elegans slow growth wormbase
CELE_ZK858.1 Caenorhabditis elegans sterile wormbase
PBANKA_1347200 Plasmodium berghei Slow plasmo
TGME49_210440 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
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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Gene identifier PF3D7_1332400 (Plasmodium falciparum), nucleotidyltransferase, putative
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