Detailed view for PF3D7_0423100

Basic information

TDR Targets ID: 4000
Plasmodium falciparum, AP-4 complex subunit sigma, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.8261 | Length (AA): 146 | MW (Da): 17449 | 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

PF01217   Clathrin adaptor complex small chain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030133   transport vesicle  
GO:0030141   secretory granule  
GO:0030117   membrane coat  
GO:0008565   protein transporter activity  
GO:0005515   protein binding  
GO:0016192   vesicle-mediated transport  
GO:0015031   protein transport  
GO:0006886   intracellular protein transport  
GO:0006810   transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
1 143 1gw5 (S) 1 142 39.00 0 1 1.65 -2.43
1 145 1w63 (Q) 1 144 40.00 0 1 1.61 -1.84
1 143 2vgl (S) 1 142 40.00 0 1 1.60205 -1.34
1 145 4p6z (S) 1 144 40.00 0 1 1.61175 -1.3
1 144 4hmy (S) 1 143 41.00 0 1 1.5509 -0.66

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, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Female Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, merozoite, Sporozoite, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 48 hs. Otto TD
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
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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.

Orthologs

Ortholog group members (OG5_130491)

Species Accession Gene Product
Arabidopsis thaliana AT2G19790   SNARE-like superfamily protein
Babesia bovis BBOV_IV010980   clathrin assembly protein small subunit, putative
Cryptosporidium parvum cgd8_4900   clathrin assembly protein, putative
Dictyostelium discoideum DDB_G0284905   adapter-related protein complex 4 sigma 1 subunit
Entamoeba histolytica EHI_045190   clathrin adaptor complex small chain, putative
Homo sapiens ENSG00000100478   adaptor-related protein complex 4, sigma 1 subunit
Mus musculus ENSMUSG00000020955   adaptor-related protein complex AP-4, sigma 1
Neospora caninum NCLIV_057490   AP-4 complex subunit sigma-1, putative
Oryza sativa 4345488   Os08g0395300
Oryza sativa 4348463   Os10g0368400
Plasmodium berghei PBANKA_0523500   AP-4 complex subunit sigma, putative
Plasmodium falciparum PF3D7_0423100   AP-4 complex subunit sigma, putative
Plasmodium knowlesi PKNH_0515000   AP-4 complex subunit sigma, putative
Plasmodium vivax PVX_090195   AP-4 complex subunit sigma, putative
Plasmodium yoelii PY06451   putative clathrin assembly protein
Trypanosoma brucei gambiense Tbg972.10.16660   clathrin assembly sigma-adaptin protein complex 4, putative
Trypanosoma brucei Tb927.10.14260   AP-4 complex subunit sigma-1, putative
Trypanosoma cruzi TcCLB.506525.104   AP-4 complex subunit sigma-1, putative
Trypanosoma cruzi TcCLB.511283.109   AP-4 complex subunit sigma-1, putative
Toxoplasma gondii TGME49_314418   clathrin adaptor complex small chain family protein
Theileria parva TP01_0763   clathrin assembly protein, putative
Trichomonas vaginalis TVAG_071140   clathrin coat assembly protein ap17, putative
Trichomonas vaginalis TVAG_283330   clathrin coat assembly protein ap19, putative

Essentiality

PF3D7_0423100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.14260 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.14260 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.14260 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.14260 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_314418 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus AP-2 complex subunit sigma 142 aa 41.0% 139 aa Compounds References
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_0423100 (Plasmodium falciparum), AP-4 complex subunit sigma, putative
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