Detailed view for PF3D7_0720100

Basic information

TDR Targets ID: 883
Plasmodium falciparum, small subunit rRNA processing protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.2728 | Length (AA): 255 | MW (Da): 30481 | 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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 12 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
26 131 1h2v (Z) 33 118 16.00 0 0.99 0.34 -0.16
35 129 1x5t (A) 8 83 12.00 0.00000000062 0.42 0.26 -0.18
19 252 4tql (A) 10 238 15.00 0.00000032 0.02 1.00895 -0.26
29 125 2e5h (A) 6 82 27.00 0.0024 1 0.518892 -0.27
31 124 4a8x (A) 159 233 21.00 0.0021 0.95 0.483127 -0.68
35 129 1x5t (A) 8 83 11.00 0.03 0.34 0.231049 0.27
51 252 4kis (A) 217 425 28.00 0.063 0.12 0.743257 1.85
1 257 4rh7 (A) 2901 3159 11.00 0.6 0 1.02712 0.32
5 129 1u6f (A) 15 116 17.00 0.00023 1 0.490696 0.34
35 69 3d2w (A) 193 227 17.00 0.32 0.13 0.226859 0.82
65 244 4o87 (A) 82 304 31.00 0.62 0.57 0.716774 0.61
172 252 1w9r (A) 6 84 13.00 0.77 0.02 0.509153 -0.93

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 - 8 hs, intra-erythrocytic - 16 hs, Oocyst, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, Male Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
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.
  • 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.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127993)

Species Accession Gene Product
Arabidopsis thaliana AT3G56510   RNA recognition motif-containing protein
Babesia bovis BBOV_IV004420   conserved hypothetical protein
Brugia malayi Bm1_49055   activator of basal transcription 1
Candida albicans CaO19.10670   similar to S. cerevisiae YNR054C
Candida albicans CaO19.3161   similar to S. cerevisiae YNR054C
Caenorhabditis elegans CELE_F57B10.8   Protein F57B10.8
Cryptosporidium hominis Chro.40089   hypothetical protein
Cryptosporidium parvum cgd4_710   Ynr054cp, basal transcriptional activator hABT1, RRM domain containing protein
Dictyostelium discoideum DDB_G0293576   RNA-binding region RNP-1 domain-containing protein
Drosophila melanogaster Dmel_CG41562   CG41562 gene product from transcript CG41562-RA
Drosophila melanogaster Dmel_CG32708   CG32708 gene product from transcript CG32708-RA
Drosophila melanogaster Dmel_CG10993   CG10993 gene product from transcript CG10993-RA
Drosophila melanogaster Dmel_CG40813   CG40813 gene product from transcript CG40813-RB
Echinococcus granulosus EgrG_000798200   RNA recognition motif RNP 1
Entamoeba histolytica EHI_174110   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000798200   RNA recognition motif, RNP 1
Giardia lamblia GL50803_3294   hypothetical protein
Homo sapiens 29777   activator of basal transcription 1
Leishmania braziliensis LbrM.34.1320   hypothetical protein, conserved
Leishmania donovani LdBPK_351410.1   hypothetical protein, conserved
Leishmania infantum LinJ.35.1410   hypothetical protein, conserved
Leishmania major LmjF.35.1400   hypothetical protein, conserved
Leishmania mexicana LmxM.34.1400   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_01569   hypothetical protein
Mus musculus 30946   activator of basal transcription 1
Neospora caninum NCLIV_005100   GD15873, related
Oryza sativa 4344189   Os07g0662600
Onchocerca volvulus OVOC865   Activator of basal transcription 1 homolog
Plasmodium berghei PBANKA_0617600   small subunit rRNA processing protein, putative
Plasmodium falciparum PF3D7_0720100   small subunit rRNA processing protein, putative
Plasmodium knowlesi PKNH_0315500   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_096315   hypothetical protein, conserved
Plasmodium yoelii PY00333   hypothetical protein
Saccharomyces cerevisiae YNR054C   Esf2p
Schistosoma japonicum Sjp_0203890   Pre-rRNA-processing protein esf2, putative
Schistosoma mansoni Smp_093850   hypothetical protein
Schmidtea mediterranea mk4.001701.06   Activator of basal transcription 1
Trypanosoma brucei gambiense Tbg972.5.1480   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.1080   RNA-binding protein, putative
Trypanosoma congolense TcIL3000_0_58080   RNA-binding protein, putative
Trypanosoma cruzi TcCLB.508299.89   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.511181.70   hypothetical protein, conserved
Theileria parva TP01_0309   hypothetical protein
Trichomonas vaginalis TVAG_122000   conserved hypothetical protein

Essentiality

PF3D7_0720100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.1080 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.1080 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.5.1080 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.5.1080 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F57B10.8 Caenorhabditis elegans larval arrest wormbase
CELE_F57B10.8 Caenorhabditis elegans slow growth wormbase
CELE_F57B10.8 Caenorhabditis elegans sterile wormbase
YNR054C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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_0720100 (Plasmodium falciparum), small subunit rRNA processing protein, putative
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