Detailed view for PF3D7_1429800

Basic information

TDR Targets ID: 2608
Plasmodium falciparum, coatomer subunit beta, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.1515 | Length (AA): 1370 | MW (Da): 159972 | 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

PF01602   Adaptin N terminal region
PF07718   Coatomer beta C-terminal region
PF14806   Coatomer beta subunit appendage platform

Gene Ontology

Mouse over links to read term descriptions.
GO:0006890   retrograde vesicle-mediated transport, Golgi to ER  
GO:0030126   COPI vesicle coat  
GO:0030117   membrane coat  
GO:0005737   cytoplasm  
GO:0005515   protein binding  
GO:0005488   binding  
GO:0005198   structural molecule activity  
GO:0016192   vesicle-mediated transport  
GO:0006886   intracellular protein transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 14 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
23 433 1wa5 (B) 88 513 8.00 0.000044 0.08 0.29 -0.33
24 1127 1u6g (C) 8 1203 10.00 0 1 0.54 0.43
8 173 4hmy (A) 15 174 14.00 0.00029 0.86 0.321968 -0.35
26 232 4hmy (B) 17 217 23.00 0 0.96 0.412395 0.02
100 279 4hmy (A) 101 283 19.00 0.27 0.93 0.391687 -0.5
551 707 4v3d (A) 528 693 30.00 0.12 0.55 0.163099 1.14
867 1050 4tql (A) 27 213 13.00 0.41 0.07 0.285107 -0.64
8 173 4hmy (A) 15 174 14.00 0.00072 0.84 0.322282 -0.45
18 1063 4rh7 (A) 1255 2285 10.00 0 0.93 0.267526 1.24
23 130 4db6 (A) 12 124 13.00 0.83 0.29 0.276059 -1.15
489 973 2nyy (A) 670 1128 25.00 0.11 0.93 0.312505 1.33
522 600 3ult (A) 35 116 27.00 0.34 0.16 0.408948 -1.09
552 708 4v3d (A) 528 693 30.00 0.13 0.55 0.160385 1.14
1117 1356 1pzd (A) 615 873 16.00 0.8 0.5 0.203876 0.32

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

Orthologs

Ortholog group members (OG5_127619)

Species Accession Gene Product
Arabidopsis thaliana AT4G31490   coatomer subunit beta-2
Arabidopsis thaliana AT4G31480   coatomer subunit beta-1
Babesia bovis BBOV_IV010410   coatamer beta subunit, putative
Brugia malayi Bm1_24795   coatomer beta subunit
Candida albicans CaO19.8161   ER-Golgi transport
Candida albicans CaO19.528   ER-Golgi transport
Caenorhabditis elegans CELE_Y25C1A.5   Protein COPB-1
Cryptosporidium hominis Chro.60040   hypothetical protein
Cryptosporidium parvum cgd6_270   hypothetical protein
Dictyostelium discoideum DDB_G0284735   adaptin N-terminal domain-containing protein
Drosophila melanogaster Dmel_CG6223   Coat Protein (coatomer) beta
Echinococcus granulosus EgrG_000777200   Coatomer subunit beta
Entamoeba histolytica EHI_027720   coatomer beta subunit, putative
Entamoeba histolytica EHI_088220   coatomer beta subunit, putative
Entamoeba histolytica EHI_173180   coatomer subunit beta, putative
Echinococcus multilocularis EmuJ_000777200   Coatomer subunit beta
Giardia lamblia GL50803_88082   Coatomer beta subunit
Homo sapiens ENSG00000129083   coatomer protein complex, subunit beta 1
Leishmania braziliensis LbrM.20.5560   coatomer beta subunit, putative
Leishmania donovani LdBPK_201390.1   coatomer beta subunit, putative
Leishmania infantum LinJ.20.1390   coatomer beta subunit, putative
Leishmania major LmjF.20.1350   coatomer beta subunit, putative
Leishmania mexicana LmxM.20.1350   coatomer beta subunit, putative
Loa Loa (eye worm) LOAG_01407   coatomer beta subunit
Mus musculus ENSMUSG00000030754   coatomer protein complex, subunit beta 1
Neospora caninum NCLIV_039080   Adaptin N terminal region family protein, related
Oryza sativa 4349913   Os11g0174000
Oryza sativa 4326915   Os01g0281400
Plasmodium berghei PBANKA_1014900   coatomer subunit beta, putative
Plasmodium falciparum PF3D7_1429800   coatomer subunit beta, putative
Plasmodium knowlesi PKNH_1328900   coatomer subunit beta, putative
Plasmodium vivax PVX_085050   coatamer protein, beta subunit, putative
Plasmodium yoelii PY01272   coatomer beta subunit
Saccharomyces cerevisiae YDR238C   Sec26p
Schistosoma japonicum Sjp_0060340   Coatomer subunit beta, putative
Schistosoma mansoni Smp_124430   coatomer beta subunit
Schmidtea mediterranea mk4.006851.00   Coatomer subunit beta
Schmidtea mediterranea mk4.020599.00   Coatomer subunit beta
Trypanosoma brucei gambiense Tbg972.1.1540   coatomer beta subunit, putative
Trypanosoma brucei Tb927.1.2570   coatomer beta subunit
Trypanosoma congolense TcIL3000_1_1330   coatomer beta subunit, putative
Trypanosoma cruzi TcCLB.506563.30   coatomer beta subunit, putative
Toxoplasma gondii TGME49_266990   beta-COP
Theileria parva TP01_0687   coatomer beta subunit, putative
Trichomonas vaginalis TVAG_366270   coatomer beta subunit, putative
Trichomonas vaginalis TVAG_150910   coatomer beta subunit, putative

Essentiality

PF3D7_1429800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.1.2570 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.1.2570 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.1.2570 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.1.2570 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y25C1A.5 Caenorhabditis elegans adult lethal wormbase
CELE_Y25C1A.5 Caenorhabditis elegans sterile wormbase
YDR238C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1014900 Plasmodium berghei Essential plasmo
TGME49_266990 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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

Druggability index (range: 0 to 1): 0.5

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_1429800 (Plasmodium falciparum), coatomer subunit beta, putative
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