Detailed view for PF3D7_1018600

Basic information

TDR Targets ID: 1255
Plasmodium falciparum, tRNA wybutosine-synthesizing protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8616 | Length (AA): 1904 | MW (Da): 227123 | 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

PF02475   Met-10+ like-protein
PF02676   Methyltransferase TYW3
PF13418   Galactose oxidase, central domain
PF13854   Kelch motif
PF13964   Kelch motif

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 21 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
299 446 1tlj (A) 26 192 22.00 0 0.32 0.15 -0.11
614 1001 1zgk (A) 324 608 15.00 0 0.99 -0.1 0.41
1508 1789 2frn (A) 19 257 24.00 0 1 -0.01 1.05
1635 1769 2gpy (A) 43 196 7.00 0.000014 0.09 0.16 -0.76
28 934 3ffz (A) 355 1247 22.00 0.18 0.77 0.328466 2.27
359 449 2it2 (A) 107 199 27.00 0.53 0.39 0.217594 0.6
430 1553 4w8f (A) 1366 2506 10.00 0 0.85 -0.0235639 1.88
1156 1388 4tql (A) 9 238 22.00 0.031 0.35 0.374174 -0.66
1307 1488 4uos (A) 1 180 24.00 0.22 0.16 0.348388 -0.76
1417 1798 2zzm (A) 4 331 27.00 0.00000000011 1 0.13743 1.94
1418 1768 2yx1 (B) 5 300 31.00 0.00042 1 0.136449 1.4
1611 1815 3a27 (A) 63 249 24.00 0.00000041 0.82 0.335368 -0.17
1627 1787 1l3i (A) 14 154 14.00 0.00006 0.85 0.131259 -0.13
19 351 3v0a (B) 788 1089 28.00 0.62 0.12 0.00829048 2.42
39 1000 3v0a (A) 248 1265 15.00 0.000000097 0.73 0.298395 2.13
279 430 2qg3 (A) 23 169 18.00 0.00000014 0.98 0.177123 0.65
291 449 2it2 (A) 30 199 20.00 0.27 0.68 0.291527 -0.3
309 438 1tlj (A) 38 184 32.00 0.0024 0.82 0.245883 0.77
1192 1383 4uos (A) 1 184 22.00 0.31 0.68 0.415987 -1.27
1400 1754 2yx1 (A) 5 300 30.00 0.00016 1 0.145931 1.54
1402 1773 2zzm (A) 8 320 27.00 0.00000000019 1 0.123225 1.83

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 60-80% percentile merozoite, sporozoite, early ring, early trophozoite, late ring, Ring, Sporozoite. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, gametocyte, late schizont, late trophozoite, Oocyst, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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.

Orthologs

Ortholog group members (OG5_129346)

Species Accession Gene Product
Arabidopsis thaliana AT4G04670   Met-10+ like family protein / kelch repeat-containing protein
Brugia malayi Bm1_51625   Met-10+ like-protein
Candida albicans CaO19.7369   similar to S. cerevisiae YML005W
Caenorhabditis elegans CELE_F40F9.10   Protein F40F9.10
Homo sapiens ENSG00000183665   tRNA methyltransferase 12 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.03.0070   hypothetical protein, conserved
Leishmania donovani LdBPK_030050.1   Met-10+ like-protein, putative
Leishmania infantum LinJ.03.0050   hypothetical protein, conserved
Leishmania major LmjF.03.0060   hypothetical protein, conserved
Leishmania mexicana LmxM.03.0060   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_02567   hypothetical protein
Loa Loa (eye worm) LOAG_14175   hypothetical protein
Mus musculus ENSMUSG00000037085   tRNA methyltranferase 12
Oryza sativa 4343372   Os07g0515000
Plasmodium berghei PBANKA_0502800   tRNA wybutosine-synthesizing protein, putative
Plasmodium falciparum PF3D7_1018600   tRNA wybutosine-synthesizing protein, putative
Plasmodium knowlesi PKNH_0602900   tRNA wybutosine-synthesizing protein, putative
Plasmodium yoelii PY05008   Unknown protein
Saccharomyces cerevisiae YML005W   Trm12p
Trypanosoma brucei gambiense Tbg972.10.3900   hypothetical protein, conserved,predicted to be involved in methionine biosynthesis
Trypanosoma brucei Tb927.10.3080   methionine biosynthetic protein, putative
Trypanosoma congolense TcIL3000_10_2530   predicted to be involved in methionine biosynthesis
Trypanosoma cruzi TcCLB.510943.180   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.504867.110   hypothetical protein, conserved
Toxoplasma gondii TGME49_234490   kelch repeat-containing protein
Theileria parva TP02_0179   hypothetical protein

Essentiality

PF3D7_1018600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3080 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.3080 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.3080 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.3080 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0502800 Plasmodium berghei Essential plasmo
TGME49_234490 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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.

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 PF3D7_1018600 (Plasmodium falciparum), tRNA wybutosine-synthesizing protein, putative
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