Detailed view for PF3D7_1214400

Basic information

TDR Targets ID: 5189
Plasmodium falciparum, ER membrane protein complex subunit 6, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6428 | Length (AA): 120 | MW (Da): 13738 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 2

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

PF07019   Rab5-interacting protein (Rab5ip)

Gene Ontology

Mouse over links to read term descriptions.
GO:0072546   GO:ER membrane protein complex  

GO:0018348   protein amino acid geranylgeranylation  
GO:0016021   integral to membrane  
GO:0005783   endoplasmic reticulum  

Metabolic Pathways

N-Glycan biosynthesis (KEGG)

Structural information

Modbase 3D models:

There are 2 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
4 520 1ld8 (B) 525 909 18.00 0 1 0.78 -0.1
89 498 1dce (B) 13 329 29.00 0 1 0.85 -0.62

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 - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 40 hs, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Oocyst, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 48 hs, late schizont. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. Lasonder E
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.
  • 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

Orthologs

Ortholog group members (OG5_129667)

Species Accession Gene Product
Arabidopsis thaliana AT5G49540   Rab5-interacting family protein
Brugia malayi Bm1_34145   RE35789p
Candida albicans CaO19.10213   similar to S. cerevisiae YLL014W
Candida albicans CaO19.2698   similar to S. cerevisiae YLL014W
Caenorhabditis elegans CELE_F33D4.7   Protein EMC-6
Dictyostelium discoideum DDB_G0280399   DUF786 family protein
Drosophila melanogaster Dmel_CG11781   CG11781 gene product from transcript CG11781-RA
Echinococcus granulosus EgrG_000847600   transmembrane protein 93
Echinococcus multilocularis EmuJ_000847600   transmembrane protein 93
Homo sapiens ENSG00000127774   ER membrane protein complex subunit 6
Leishmania braziliensis LbrM.32.3270   hypothetical protein, conserved
Leishmania donovani LdBPK_323170.1   Rab5-interacting protein (Rab5ip), putative
Leishmania infantum LinJ.32.3170   hypothetical protein, conserved
Leishmania major LmjF.32.2995   hypothetical protein, conserved
Leishmania mexicana LmxM.31.2995   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_09031   hypothetical protein
Mus musculus ENSMUSG00000047260   ER membrane protein complex subunit 6
Neospora caninum NCLIV_016310   hypothetical protein, conserved
Oryza sativa 4324140   Os01g0683600
Plasmodium berghei PBANKA_1430200   ER membrane protein complex subunit 6, putative
Plasmodium falciparum PF3D7_1214400   ER membrane protein complex subunit 6, putative
Saccharomyces cerevisiae YLL014W   Emc6p
Schistosoma mansoni Smp_068580.1   hypothetical protein
Schmidtea mediterranea mk4.012023.00   ER membrane protein complex subunit 6
Trypanosoma brucei gambiense Tbg972.11.19200   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.17010   Rab5-interacting protein (Rab5ip), putative
Trypanosoma cruzi TcCLB.511541.30   Rab5-interacting protein (Rab5ip), putative
Trypanosoma cruzi TcCLB.508707.280   Rab5-interacting protein (Rab5ip), putative
Toxoplasma gondii TGME49_239690   hypothetical protein

Essentiality

PF3D7_1214400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.8775 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.8775 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.8775 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.8775 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F33D4.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_F33D4.7 Caenorhabditis elegans larval arrest wormbase
TGME49_239690 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
  • 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.
  • 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
  • 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.
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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

Druggability index (range: 0 to 1): 0.4

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

14 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PF3D7_1214400 (Plasmodium falciparum), ER membrane protein complex subunit 6, putative
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