Detailed view for PF3D7_0933800

Basic information

TDR Targets ID: 5008
Plasmodium falciparum, tubulin delta chain, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.5882 | Length (AA): 735 | MW (Da): 86520 | Paralog Number: 0

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

Druggability Group : DG3

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

PF00091   Tubulin/FtsZ family, GTPase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0043234   protein complex  
GO:0005874   microtubule  
GO:0005525   GTP binding  
GO:0005200   structural constituent of cytoskeleton  
GO:0005198   structural molecule activity  
GO:0003924   GTPase activity  
GO:0051258   protein polymerization  
GO:0007018   microtubule-based movement  
GO:0007017   microtubule-based process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 9 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
226 567 1w5b (A) 25 348 12.00 0 0.97 0.47 -0.67
228 735 2bto (A) 24 432 16.00 0 0.88 0.36 0.37
203 646 4i4t (B) 14 435 20.00 0 1 0.706082 0.42
274 489 2btq (B) 86 303 30.00 0 0.65 0.522978 0.36
274 521 2btq (B) 86 339 26.00 0 0.94 0.574415 0.21
314 421 3zid (A) 95 198 30.00 0.0047 0.43 0.448039 -0.18
203 732 2btq (A) 24 433 15.00 0 1 0.385244 0.96
271 487 2btq (B) 86 304 28.00 0 0.95 0.566248 0.03
311 418 3zid (A) 95 198 30.00 0.0032 0.45 0.469541 -0.38

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 Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 32 hs, gametocyte, early schizont, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Ring, Sporozoite. Otto TD Zanghi G
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_132171)

Species Accession Gene Product
Babesia bovis BBOV_III004980   conserved hypothetical protein
Echinococcus granulosus EgrG_000877100   tubulin delta chain
Echinococcus multilocularis EmuJ_000877100   tubulin delta chain
Giardia lamblia GL50803_5462   Delta tubulin
Homo sapiens ENSG00000108423   tubulin, delta 1
Mus musculus ENSMUSG00000020513   tubulin, delta 1
Plasmodium berghei PBANKA_0834600   tubulin delta chain, putative
Plasmodium falciparum PF3D7_0933800   tubulin delta chain, putative
Plasmodium knowlesi PKNH_0000900   delta tubulin, putative
Plasmodium knowlesi PKNH_0732500   tubulin delta chain, putative
Plasmodium vivax PVX_087025   delta tubulin, putative
Plasmodium yoelii PY01830   similar to delta-tubulin-related
Schistosoma japonicum Sjp_0203470   ko:K10390 tubulin delta, putative
Schistosoma mansoni Smp_154880   tubulin subunit delta
Schmidtea mediterranea mk4.001116.02   TUBD1
Trichomonas vaginalis TVAG_207590   tubulin gamma chain, putative

Essentiality

PF3D7_0933800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0834600 Plasmodium berghei Dispensable plasmo
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
  • 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
  • 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

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0101 0.3552 0
0.0026 0.2908 0
0.0068 0.2651 0.2578
0.0563 0.2544 0.2544
0.0551 0.2529 0
0.0034 0.3051 0.3051
0.0066 0.35 0.2921
0.0546 0.2544 0.2542
0.0525 0.2545 0.2544
0.0561 0.2529 0
0.0054 0.2833 0.2833
0.0535 0.2519 0
0.0047 0.2592 0.2592
0.04 0.2514 0
0.0406 0.2514 0.2514
0.056 0.2514 0.2514
0.0546 0.2545 0.2542
0.0085 0.3918 0
0.0538 0.2536 0.2531
0.0045 0.3536 0.2538
0.0848 0.2545 0.2529
0.004 0.2973 0.2973
0.0045 0.2537 0.2537
0.0092 0.4079 0
0.0074 0.4006 0.3795
0.0069 0.3392 0.3392
0.0045 0.2572 0.2572
0.0729 0.2541 0.2529
0.0402 0.2538 0.2529
0.0043 0.4107 0.333
0.085 0.2537 0.2521
0.0072 0.4058 0.4058
0.0403 0.2536 0.2466
0.0409 0.2544 0.2542
0.0402 0.2538 0.2529
0.0843 0.2537 0.2522
0.0302 0.2563 0.2529
0.0051 0.3883 0
0.0546 0.2544 0.2542
0.0067 0.252 0
0.0401 0.2516 0.2496
0.0046 0.3108 0.3108
0.0054 0.2826 0.2826
0.0719 0.2541 0
0.0546 0.2545 0.2542
0.0723 0.2529 0.2526
0.0684 0.253 0.2529
0.0428 0.2516 0.2516
0.0102 0.3953 0
0.0284 0.2518 0.2518
0.0407 0.2502 0.2449
0.0222 0.2501 0.2496
0.0849 0.2532 0.2532
0.0265 0.2509 0.2507
0.0057 0.393 0
0.0083 0.2616 0.2361
0.0841 0.2551 0.2551
0.0126 0.2524 0.3882
0.0402 0.2538 0.2529
0.0525 0.2545 0.2544
0.0046 0.2632 0.2632
0.0069 0.3392 0.3392
0.0402 0.2538 0.2529
0.0546 0.2545 0.2542

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 PF3D7_0933800 (Plasmodium falciparum), tubulin delta chain, putative
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