Detailed view for PF3D7_0828000

Basic information

TDR Targets ID: 678
Plasmodium falciparum, rhomboid protease ROM3
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.4569 | Length (AA): 267 | MW (Da): 30685 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 8

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

PF01694   Rhomboid family

Gene Ontology

Mouse over links to read term descriptions.
GO:0016021   integral to membrane  
GO:0004252   serine-type endopeptidase activity  
GO:0006508   proteolysis  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
42 259 3d31 (C) 13 258 16.00 0.15 0.04 0.514579 1.87

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 gametocyte, Female Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile merozoite, sporozoite, early ring, early schizont. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile early trophozoite, late ring, late schizont, late trophozoite, Sporozoite, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, Oocyst. Otto TD Zanghi G
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
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127224)

Species Accession Gene Product
Arabidopsis thaliana AT5G07250   RHOMBOID-like protein 3
Arabidopsis thaliana AT1G63120   rhomboid -like 2
Arabidopsis thaliana AT2G29050   protein RHOMBOID-like 1
Arabidopsis thaliana AT1G12750   RHOMBOID-like protein 6
Arabidopsis thaliana AT3G53780   RHOMBOID-like protein 4
Arabidopsis thaliana AT1G25290   RHOMBOID-like protein 10
Brugia malayi Bm1_50620   Rhomboid family protein
Candida albicans CaO19.5234   similar to N. crassa orf (NCU01305.1)
Candida albicans CaO19.12698   similar to N. crassa orf (NCU01305.1)
Caenorhabditis elegans CELE_Y116A8C.16   Protein ROM-4, isoform D
Caenorhabditis elegans CELE_Y116A8C.14   Protein ROM-3
Dictyostelium discoideum DDB_G0295849   rhomboid family protein
Drosophila melanogaster Dmel_CG33304   rhomboid-5
Echinococcus granulosus EgrG_001179900   inactive rhomboid protein 1
Entamoeba histolytica EHI_197460   peptidase S54 (rhomboid) family protein
Echinococcus multilocularis EmuJ_001179900   inactive rhomboid protein 1
Homo sapiens ENSG00000129667   rhomboid 5 homolog 2 (Drosophila)
Homo sapiens ENSG00000007384   rhomboid 5 homolog 1 (Drosophila)
Loa Loa (eye worm) LOAG_05867   rhomboid family protein
Mus musculus ENSMUSG00000020806   rhomboid 5 homolog 2 (Drosophila)
Mus musculus ENSMUSG00000020282   rhomboid family 1 (Drosophila)
Mycobacterium tuberculosis Rv0110   Probable conserved integral membrane protein
Mycobacterium ulcerans MUL_4822   serine protease
Neospora caninum NCLIV_013010   Rhomboid family 1 (Predicted), related
Oryza sativa 4347244   Os09g0454100
Oryza sativa 4351216   Os11g0704800
Oryza sativa 4331402   Os03g0116400
Oryza sativa 4346228   Os08g0546700
Oryza sativa 4349148   Os10g0521900
Oryza sativa 4347634   Os09g0525900
Oryza sativa 9266563   Os01g0147300
Oryza sativa 4336706   Os04g0569300
Onchocerca volvulus OVOC7140  
Plasmodium berghei PBANKA_0702700   rhomboid protease ROM3
Plasmodium falciparum PF3D7_0828000   rhomboid protease ROM3
Plasmodium knowlesi PKNH_1322100   rhomboid protease ROM3, putative
Plasmodium vivax PVX_088955   rhomboid protease ROM3, putative
Plasmodium yoelii PY01364   Rhomboid family, putative
Schistosoma japonicum Sjp_0086430   IPR002610,Peptidase S54, rhomboid,domain-containing
Schistosoma japonicum Sjp_0311210   IPR002610,Peptidase S54, rhomboid,domain-containing
Schistosoma mansoni Smp_008620   RHBDF1 protein (S54 family)
Schmidtea mediterranea mk4.002600.00   Inactive rhomboid protein 1
Schmidtea mediterranea mk4.001748.02   Inactive rhomboid protein 1
Toxoplasma gondii TGME49_212910   rhomboid protease ROM3
Trichomonas vaginalis TVAG_112900   Clan S-, family S54, Rhomboid-like serine peptidase
Trichomonas vaginalis TVAG_282180   Clan S-, family S54, Rhomboid-like serine peptidase
Trichomonas vaginalis TVAG_161010   Clan S-, family S54, Rhomboid-like serine peptidase
Trichomonas vaginalis TVAG_378960   Clan S-, family S54, Rhomboid-like serine peptidase
Trichomonas vaginalis TVAG_233140   Clan S-, family S54, Rhomboid-like serine peptidase
Trichomonas vaginalis TVAG_359500   Clan S-, family S54, Rhomboid-like serine peptidase

Essentiality

PF3D7_0828000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu111 Mycobacterium tuberculosis non-essential nmpdr
PBANKA_0702700 Plasmodium berghei Dispensable plasmo
TGME49_212910 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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.
  • 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
  • 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
  • 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.

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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Gene identifier PF3D7_0828000 (Plasmodium falciparum), rhomboid protease ROM3
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