Detailed view for PF3D7_0508800

Basic information

TDR Targets ID: 4119
Plasmodium falciparum, single-stranded DNA-binding protein
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.4032 | Length (AA): 284 | MW (Da): 33860 | Paralog Number: 0

Signal peptide: Y | 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

PF00436   Single-strand binding protein family

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0003697   single-stranded DNA binding  
GO:0006260   DNA replication  

Metabolic Pathways

DNA replication (KEGG)
Mismatch repair (KEGG)
Homologous recombination (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
29 183 1se8 (A) 81 230 22.00 0 1 0.52 0.84
81 194 1z9f (A) 3 108 34.00 0 1 0.46 -0.74
77 194 3ulp (A) 77 194 99.99 0 1 1.58399 -1.04
78 225 1qvc (A) 1 144 31.00 0 1 0.858827 0.43

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:

PDB tag
  • 3ULP:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Oocyst. Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, Female Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early schizont, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 24 hs, late trophozoite, Male Gametocyte. Otto TD PlasmoDB 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.
  • 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.

Orthologs

Ortholog group members (OG5_127389)

Species Accession Gene Product
Arabidopsis thaliana AT3G18580   single-strand DNA-binding protein
Arabidopsis thaliana AT4G11060   mitochondrially targeted single-stranded DNA binding protein
Candida albicans CaO19.2483   single-stranded zinc finger DNA-binding protein
Candida albicans CaO19.10019   single-stranded zinc finger DNA-binding protein
Caenorhabditis elegans CELE_PAR2.1   Protein MTSS-1
Chlamydia trachomatis CT_044   single-stranded DNA-binding protein
Dictyostelium discoideum DDB_G0292230   hypothetical protein
Drosophila melanogaster Dmel_CG4337   mitochondrial single stranded DNA-binding protein
Escherichia coli b4059   single-stranded DNA-binding protein
Echinococcus granulosus EgrG_001119700   single strand binding protein
Echinococcus multilocularis EmuJ_001119700   single strand binding protein
Homo sapiens ENSG00000106028   single-stranded DNA binding protein 1, mitochondrial
Mycobacterium leprae ML2684c   PROBABLE SINGLE-STRAND BINDING PROTEIN SSB (HELIX-DESTABILIZING PROTEIN)
Mus musculus ENSMUSG00000029911   single-stranded DNA binding protein 1
Mycobacterium tuberculosis Rv0054   Single-strand binding protein Ssb (helix-destabilizing protein)
Mycobacterium ulcerans MUL_0072   single-stranded DNA-binding protein
Neospora caninum NCLIV_006840   hypothetical protein
Oryza sativa 4335578   Os04g0363700
Oryza sativa 4339275   Os05g0509700
Oryza sativa 4326564   Os01g0642900
Plasmodium berghei PBANKA_1108400   single-stranded DNA-binding protein, putative
Plasmodium falciparum PF3D7_0508800   single-stranded DNA-binding protein
Plasmodium knowlesi PKNH_1024800   single-stranded DNA-binding protein, putative
Plasmodium vivax PVX_098000   single-strand binding protein, putative
Plasmodium yoelii PY05238   SINGLE-STRAND BINDING PROTEIN
Saccharomyces cerevisiae YCR028C-A   Rim1p
Toxoplasma gondii TGME49_297940   single-strand binding protein
Treponema pallidum TP0062   single-strand DNA binding protein (ssb)
Wolbachia endosymbiont of Brugia malayi Wbm0211   single-stranded DNA-binding protein, ssb

Essentiality

PF3D7_0508800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b4059 Escherichia coli essential goodall
PBANKA_1108400 Plasmodium berghei Slow plasmo
TGME49_297940 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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.

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_0508800 (Plasmodium falciparum), single-stranded DNA-binding protein
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