Detailed view for PF3D7_0622200

Basic information

TDR Targets ID: 4571
Plasmodium falciparum, radical SAM protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.6843 | Length (AA): 860 | MW (Da): 99459 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF00919   Uncharacterized protein family UPF0004
PF04055   Radical SAM superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0051539   4 iron, 4 sulfur cluster binding  
GO:0051536   iron-sulfur cluster binding  
GO:0016740   transferase activity  
GO:0003824   catalytic activity  
GO:0006400   tRNA modification  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
534 822 1olt (A) 4 313 10.00 0 0.89 0.29 -0.13
546 839 1olt (A) 35 323 12.00 0 0.69 0.49 -0.56
24 188 4u5a (A) 61 238 19.00 0.44 0.17 0.37226 -0.46
24 174 4u5a (C) 61 238 23.00 0.075 0.29 0.355981 -0.44
159 502 1zro (A) 234 598 25.00 0.36 0.98 0.407 1.13
210 325 4nxj (A) 2 116 19.00 0.38 0.34 0.308284 -0.22
430 860 4jc0 (A) 2 431 22.00 0 1 0.370663 0.5

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, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Sporozoite, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, Male Gametocyte. Otto TD 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.

Orthologs

Ortholog group members (OG5_126807)

Species Accession Gene Product
Arabidopsis thaliana AT1G72090   Methylthiotransferase
Arabidopsis thaliana AT4G36390   Methylthiotransferase
Brugia malayi Bm1_47290   CDK5RAP1-like protein
Brugia malayi Bm1_17180   MiaB-like tRNA modifying enzyme, archaeal-type family protein
Caenorhabditis elegans CELE_Y92H12BL.1   Protein Y92H12BL.1
Caenorhabditis elegans CELE_F25B5.5   Protein F25B5.5
Cryptosporidium hominis Chro.60189   transmembrane protein
Cryptosporidium parvum cgd6_1520   2-methylthioadenine synthetase; MiaB
Dictyostelium discoideum DDB_G0287079   hypothetical protein
Drosophila melanogaster Dmel_CG6345   CG6345 gene product from transcript CG6345-RA
Drosophila melanogaster Dmel_CG6550   CG6550 gene product from transcript CG6550-RA
Escherichia coli b0661   tRNA-i(6)A37 methylthiotransferase
Echinococcus granulosus EgrG_000095000   CDK5 regulatory subunit associated protein
Echinococcus granulosus EgrG_000463000   cdk5 regulatory subunit associated protein 1
Entamoeba histolytica EHI_141830   RNA modification enzymes, MiaB-family
Echinococcus multilocularis EmuJ_000095000   CDK5 regulatory subunit associated protein
Echinococcus multilocularis EmuJ_000463000   cdk5 regulatory subunit associated protein 1
Giardia lamblia GL50803_102963   tRNA 2-methylthioadenosine synthase
Homo sapiens ENSG00000101391   CDK5 regulatory subunit associated protein 1
Homo sapiens ENSG00000145996   CDK5 regulatory subunit associated protein 1-like 1
Loa Loa (eye worm) LOAG_05234   CDK5 regulatory subunit-associated protein 1-like 1
Loa Loa (eye worm) LOAG_08525   hypothetical protein
Mycobacterium leprae ML0989   CONSERVED HYPOTHETICAL ALANINE, ARGININE-RICH PROTEIN
Mus musculus ENSMUSG00000006191   CDK5 regulatory subunit associated protein 1-like 1
Mus musculus ENSMUSG00000027487   CDK5 regulatory subunit associated protein 1
Mycobacterium tuberculosis Rv2733c   Conserved hypothetical alanine, arginine-rich protein
Mycobacterium ulcerans MUL_3378   (dimethylallyl)adenosine tRNA methylthiotransferase
Neospora caninum NCLIV_034370   radical SAM domain-containing protein, putative
Oryza sativa 4350829   Os11g0592800
Oryza sativa 4335891   Os04g0434300
Onchocerca volvulus OVOC13462  
Onchocerca volvulus OVOC13432  
Onchocerca volvulus OVOC7313  
Plasmodium berghei PBANKA_1121100   radical SAM protein, putative
Plasmodium falciparum PF3D7_0622200   radical SAM protein, putative
Plasmodium knowlesi PKNH_1128000   radical SAM protein, putative
Plasmodium vivax PVX_114225   tRNA modifying enzyme, putative
Plasmodium yoelii PY01291   Drosophila melanogaster GH28477p-related
Schistosoma japonicum Sjp_0113300   ko:K06168 bifunctional enzyme involved in thiolation and methylation of tRNA, putative
Schistosoma japonicum Sjp_0028130   Trafficking protein particle complex subunit 5, putative
Schistosoma japonicum Sjp_0028140   CDK5 regulatory subunit-associated protein 1-like 1, putative
Schistosoma japonicum Sjp_0127690   CDK5RAP1-like protein, putative
Schistosoma mansoni Smp_192180   radical sam proteins
Schistosoma mansoni Smp_147410   radical sam proteins
Schistosoma mansoni Smp_152690   radical sam proteins
Schmidtea mediterranea mk4.001192.08   CDK5RAP1-like protein
Schmidtea mediterranea mk4.000558.08   Radical sam proteins, putative
Trypanosoma brucei gambiense Tbg972.6.3270   tRNA modification enzyme, putative
Trypanosoma brucei Tb11.v5.0635   tRNA modification enzyme, putative
Trypanosoma brucei Tb927.6.3510   tRNA modification enzyme, putative
Trypanosoma congolense TcIL3000_6_3050   tRNA modification enzyme, putative
Trypanosoma cruzi TcCLB.511511.20   tRNA modification enzyme, putative
Trypanosoma cruzi TcCLB.506941.20   tRNA modification enzyme, putative
Toxoplasma gondii TGME49_273140   radical SAM methylthiotransferase, MiaB/RimO family protein
Treponema pallidum TP0269   hypothetical protein
Treponema pallidum TP0754   (dimethylallyl)adenosine tRNA methylthiotransferase
Theileria parva TP04_0588   hypothetical protein, conserved
Wolbachia endosymbiont of Brugia malayi Wbm0364   (dimethylallyl)adenosine tRNA methylthiotransferase
Wolbachia endosymbiont of Brugia malayi Wbm0101   2-methylthioadenine synthetase

Essentiality

PF3D7_0622200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2779 Mycobacterium tuberculosis non-essential nmpdr
Tb927.6.3510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.3510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.3510 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.3510 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0661 Escherichia coli non-essential goodall
CELE_Y92H12BL.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y92H12BL.1 Caenorhabditis elegans larval arrest wormbase
CELE_Y92H12BL.1 Caenorhabditis elegans slow growth wormbase
PBANKA_1121100 Plasmodium berghei Dispensable plasmo
TGME49_273140 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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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Gene identifier PF3D7_0622200 (Plasmodium falciparum), radical SAM protein, putative
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