Detailed view for PF3D7_1124100

Basic information

TDR Targets ID: 1721
Plasmodium falciparum, beige/BEACH domain protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.7116 | Length (AA): 1653 | MW (Da): 195835 | 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

PF02138   Beige/BEACH domain

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 11 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
477 885 1t77 (A) 2084 2489 32.00 0 1 0.28 -0.7
112 378 4wat (A) 192 464 30.00 0.5 0.75 0.164125 0.88
132 312 4uos (A) 10 184 13.00 0.059 0.04 0.351098 -1.74
373 1586 3v0a (B) 1 1182 24.00 0.17 1 0.610022 1.8
480 882 1t77 (A) 2087 2486 34.00 0 1 0.465399 0.04
1209 1643 3ffz (A) 797 1246 24.00 0.005 0.7 0.158758 1.6
1402 1508 3ult (A) 6 107 20.00 0.017 0.21 0.190331 -0.01
185 468 4o87 (A) 14 291 26.00 0.21 0.39 0.231498 0.54
247 434 4uos (A) 2 183 12.00 0.072 0.02 0.272927 -1.13
474 885 1mi1 (A) 2145 2553 32.00 0 1 0.450092 -0.11
1415 1472 3ult (A) 20 80 45.00 0.0017 1 0.671024 -1.51

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

Orthologs

Ortholog group members (OG5_130409)

Species Accession Gene Product
Babesia bovis BBOV_IV002430   factor associated with neutral-sphingomyelinase activation
Cryptosporidium hominis Chro.40385   hypothetical protein
Cryptosporidium parvum cgd4_3390   neutral sphingomyelinase activation associated factor-like BEACH domain containing protein
Dictyostelium discoideum DDB_G0284333   BEACH domain-containing protein
Entamoeba histolytica EHI_056360   hypothetical protein, conserved domain containing
Homo sapiens ENSG00000035681   neutral sphingomyelinase (N-SMase) activation associated factor
Leishmania braziliensis LbrM.23.1810   neutral sphingomyelinase activation associated factor-like protein
Leishmania donovani LdBPK_231970.1   neutral sphingomyelinase activation associated factor-like protein
Leishmania infantum LinJ.23.1970   neutral sphingomyelinase activation associated factor-like protein
Leishmania major LmjF.23.1570   neutral sphingomyelinase activation associated factor-like protein
Leishmania mexicana LmxM.23.1570   neutral sphingomyelinase activation associated factor-like protein
Mus musculus ENSMUSG00000028245   neutral sphingomyelinase (N-SMase) activation associated factor
Neospora caninum NCLIV_024920   hypothetical protein
Plasmodium berghei PBANKA_0924200   beige/BEACH domain protein, putative
Plasmodium falciparum PF3D7_1124100   beige/BEACH domain protein, putative
Plasmodium knowlesi PKNH_0921900   beige/BEACH domain protein, putative
Plasmodium vivax PVX_091820   hypothetical protein, conserved
Plasmodium yoelii PY01158   protein factor associated with neutral-sphingomyelinase activation
Toxoplasma gondii TGME49_263000   Beige/BEACH domain-containing protein
Theileria parva TP03_0409   hypothetical protein

Essentiality

PF3D7_1124100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
TGME49_263000 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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.
  • 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 PF3D7_1124100 (Plasmodium falciparum), beige/BEACH domain protein, putative
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