Detailed view for PF3D7_1033700

Basic information

TDR Targets ID: 1402
Plasmodium falciparum, bromodomain protein 1
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.3349 | Length (AA): 488 | MW (Da): 55937 | 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

PF00439   Bromodomain
PF12796   Ankyrin repeats (3 copies)

Gene Ontology

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

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 13 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
7 275 1n11 (A) 536 770 20.00 0 1 0.68 0.14
130 216 1ycs (B) 331 417 29.00 0.000015 1 0.71 -1.53
293 434 2fsa (A) 32 169 28.00 0.00000018 1 0.73 -0.9
333 438 1x0j (A) 76 181 29.00 0 1 0.8 -2.09
4 105 2xeh (A) 44 125 32.00 0.00000000026 1 0.430516 -0.57
4 100 2dzn (A) 69 147 24.00 0.00097 0.92 0.36327 -0.68
9 70 3d9h (A) 71 132 16.00 0.4 0.09 0.432549 -1.49
11 199 4g8k (A) 29 209 30.00 0.000073 1 0.658195 -0.28
63 235 4qfv (A) 13 187 36.00 0 1 0.809408 -0.82
126 223 3c5r (A) 428 524 33.00 0.00029 1 0.77972 -1.76
133 215 1s70 (B) 47 129 35.00 0.0035 1 0.739982 -1.37
333 455 3fkm (X) 333 455 99.99 0 1 1.42195 -1.27
333 455 3fkm (X) 333 455 99.99 0 1 1.43305 -1.38

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:

PDB tag
  • 3FKM:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5ULC:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Oocyst, Ring, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, late schizont, Sporozoite, Male Gametocyte. Otto TD 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
  • 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.

Orthologs

Ortholog group members (OG5_135777)

Species Accession Gene Product
Babesia bovis BBOV_IV010270   bromodomain/ankyrin repeat containing protein
Cryptosporidium hominis Chro.50328   hypothetical protein
Cryptosporidium parvum cgd5_630   protein with 4 ankyrin repeats plus a bromodomain.
Neospora caninum NCLIV_024360   hypothetical protein
Plasmodium berghei PBANKA_0517500   bromodomain protein 1, putative
Plasmodium falciparum PF3D7_1033700   bromodomain protein 1
Plasmodium knowlesi PKNH_0618500   bromodomain protein 1, putative
Plasmodium vivax PVX_111040   hypothetical protein, conserved
Plasmodium yoelii PY03147   hypothetical protein
Plasmodium yoelii PY03146   similar to S. cerevisiae BDF1
Toxoplasma gondii TGME49_263580   bromodomain-containing protein
Theileria parva TP01_0784   hypothetical protein

Essentiality

PF3D7_1033700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0517500 Plasmodium berghei Essential plasmo
TGME49_263580 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • 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.
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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_1033700 (Plasmodium falciparum), bromodomain protein 1
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