Detailed view for PF3D7_0921800

Basic information

TDR Targets ID: 4893
Plasmodium falciparum, ribosome production factor 1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.3078 | Length (AA): 328 | MW (Da): 39170 | Paralog Number: 0

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

Druggability Group : DG2

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

PF04427   Brix domain

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
123 212 2cxh (A) 15 107 23.00 0.000000000016 0.38 0.53 -1.13
2 163 4uos (A) 2 176 14.00 0.063 0 0.584002 -0.45
119 312 5a53 (C) 25 250 16.00 0 0.31 0.635563 0.02
2 175 4uos (A) 2 184 13.00 0.16 0.01 0.672188 -0.72

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 - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, gametocyte, merozoite, sporozoite, early ring, early trophozoite, late ring, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 48 hs, early schizont, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • 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_128253)

Species Accession Gene Product
Arabidopsis thaliana AT4G01560   protein MATERNAL EFFECT EMBRYO ARREST 49
Babesia bovis BBOV_IV002520   RNA processing factor 1, putative
Brugia malayi Bm1_43415   Brix domain containing protein
Candida albicans CaO19.2667   brix domain protein similar to S. cerevisiae RPF1 (YHR088W) nucleolar protein involved in 60S ribosomal subunit biogenesis
Candida albicans CaO19.10184   brix domain protein similar to S. cerevisiae RPF1 (YHR088W) nucleolar protein involved in 60S ribosomal subunit biogenesis
Caenorhabditis elegans CELE_F44G4.1   Protein F44G4.1
Cryptosporidium hominis Chro.20022   hypothetical protein
Cryptosporidium parvum cgd2_160   IMP4-like U3 small nucleolar ribonucleoprotein (snoRNP)
Dictyostelium discoideum DDB_G0285829   brix domain-containing protein
Drosophila melanogaster Dmel_CG6712   CG6712 gene product from transcript CG6712-RA
Echinococcus granulosus EgrG_000592900   ribosome production factor 1
Entamoeba histolytica EHI_126010   ribosome biogenesis protein, putative
Echinococcus multilocularis EmuJ_000592900   ribosome production factor 1
Giardia lamblia GL50803_17112   U3 small nucleolar ribonucleoprotein protein IMP4, putative
Homo sapiens 80135   ribosome production factor 1 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.27.0540   RNA processing factor 1, putative,ribosome biogenesis protein
Leishmania donovani LdBPK_270460.1   ribosome production factor 1, putative
Leishmania infantum LinJ.27.0460   RNA processing factor 1, putative,ribosome biogenesis protein
Leishmania major LmjF.27.0450   RNA processing factor 1, putative,ribosome biogenesis protein
Leishmania mexicana LmxM.27.0450   RNA processing factor 1, putative,ribosome biogenesis protein
Loa Loa (eye worm) LOAG_06925   brix domain-containing protein
Mus musculus ensembl-mmu:ENSMUSG00000028187   ribosome production factor 1 homolog (S. cerevisiae)
Neospora caninum NCLIV_066680   hypothetical protein
Oryza sativa 4340048   Os06g0137500
Onchocerca volvulus OVOC10541   Putative ribosome production factor 1
Plasmodium berghei PBANKA_0822700   ribosome production factor 1, putative
Plasmodium falciparum PF3D7_0921800   ribosome production factor 1, putative
Plasmodium knowlesi PKNH_0719800   ribosome production factor 1, putative
Plasmodium vivax PVX_099507   hypothetical protein, conserved
Saccharomyces cerevisiae YHR088W   Rpf1p
Schistosoma japonicum Sjp_0212760   Ribosome production factor 1, putative
Schistosoma mansoni Smp_145800   U3 small nucleolar ribonucleoprotein protein imp4
Schmidtea mediterranea mk4.011562.00   Probable ribosome production factor 1
Schmidtea mediterranea mk4.007152.00   Probable ribosome production factor 1
Trypanosoma brucei gambiense Tbg972.11.1130   RNA processing factor 1, putative,ribosome biogenesis protein
Trypanosoma brucei Tb927.11.1050   ribosome production factor 1, putative
Trypanosoma congolense TcIL3000.11.990   ribosome production factor 1, putative
Trypanosoma cruzi TcCLB.506925.510   ribosome production factor 1, putative
Toxoplasma gondii TGME49_251600   IMP4 family U3 small nucleolar ribonucleoprotein (snoRNP), putative
Theileria parva TP03_0398   hypothetical protein, conserved
Trichomonas vaginalis TVAG_495410   U3 small nucleolar ribonucleoprotein imp4, putative

Essentiality

PF3D7_0921800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.03.0050 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.03.0050 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.03.0050 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.03.0050 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F44G4.1 Caenorhabditis elegans larval arrest wormbase
CELE_F44G4.1 Caenorhabditis elegans slow growth wormbase
YHR088W Saccharomyces cerevisiae inviable yeastgenome
TGME49_251600 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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

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_0921800 (Plasmodium falciparum), ribosome production factor 1, putative
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