Detailed view for PF3D7_0110800

Basic information

TDR Targets ID: 3227
Plasmodium falciparum, transcription initiation factor TFIIB, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.7201 | Length (AA): 367 | MW (Da): 42002 | 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

PF00382   Transcription factor TFIIB repeat
PF08271   TFIIB zinc-binding

Gene Ontology

Mouse over links to read term descriptions.
GO:0006355   regulation of transcription, DNA-dependent  
GO:0070897   GO:DNA-templated transcriptional preinitiation complex assembly  

GO:0017025   TATA-binding protein binding  
GO:0005667   transcription factor complex  
GO:0005634   nucleus  
GO:0005515   protein binding  
GO:0003743   translation initiation factor activity  
GO:0003702   RNA polymerase II transcription factor activity  
GO:0030528   transcription regulator activity  
GO:0008270   zinc ion binding  
GO:0006352   transcription initiation  
GO:0045449   regulation of transcription  
GO:0006413   translational initiation  
GO:0006367   transcription initiation from RNA polymerase II promoter  

Metabolic Pathways

Basal transcription factors (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
66 112 1dl6 (A) 13 58 39.00 0.000000071 0.77 0.44 1.16
150 354 2f2c (A) 41 247 17.00 0 1 0.82 -1.09
162 358 1ais (B) 1108 1298 21.00 0 1 0.82 -1.48
16 48 2emz (A) 9 41 9.00 0.026 0.04 0.326118 -1.52
16 46 2els (A) 6 36 23.00 0.97 0.13 0.439669 -1.22
46 94 1dl6 (A) 11 58 38.00 0.0025 0.9 0.513115 0.63
141 356 1c9b (A) 110 315 20.00 0 1 0.902756 -0.64

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 - 24 hs, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, Oocyst. Otto TD PlasmoDB Zanghi G
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • 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_127288)

Species Accession Gene Product
Arabidopsis thaliana AT2G41630   transcription initiation factor IIB-1
Arabidopsis thaliana AT3G10330   transcription initiation factor IIB-2
Babesia bovis BBOV_II007500   transcription initiation factor TFIIB, putative
Brugia malayi Bm1_51845   Transcription initiation factor IIB
Candida albicans CaO19.3059   one of two genes similar to S. cerevisiae SUA7 (YPR086W) RNA Pol II transcription factor TFIIB
Candida albicans CaO19.10577   one of two genes similar to S. cerevisiae SUA7 (YPR086W) RNA Pol II transcription factor TFIIB
Candida albicans CaO19.3519   one of two genes similar to S. cerevisiae SUA7 (YPR086W) RNA Pol II transcription factor TFIIB
Caenorhabditis elegans CELE_W03F9.5   Protein TTB-1
Cryptosporidium parvum cgd8_880   transcription initiation factor TFIIB Sua7p; ZnR+2cyclins
Dictyostelium discoideum DDB_G0290929   transcription initiation factor IIB
Drosophila melanogaster Dmel_CG5193   Transcription factor IIB
Echinococcus granulosus EgrG_000898300   transcription initiation factor TFIIB
Entamoeba histolytica EHI_050980   hypothetical protein
Echinococcus multilocularis EmuJ_000898300   transcription initiation factor TFIIB
Homo sapiens ENSG00000137947   general transcription factor IIB
Loa Loa (eye worm) LOAG_09807   transcription initiation factor IIB
Mus musculus ENSMUSG00000028271   general transcription factor IIB
Neospora caninum NCLIV_012900   At4g37010, related
Oryza sativa 4347689   Os09g0534800
Onchocerca volvulus OVOC12424   Transcription initiation factor IIB homolog
Plasmodium berghei PBANKA_0202900   transcription initiation factor TFIIB, putative
Plasmodium falciparum PF3D7_0110800   transcription initiation factor TFIIB, putative
Plasmodium knowlesi PKNH_0203100   transcription initiation factor TFIIB, putative
Plasmodium vivax PVX_081260   transcription initiation factor TFIIB, putative
Plasmodium yoelii PY06502   hypothetical protein
Plasmodium yoelii PY07322   hypothetical protein
Saccharomyces cerevisiae YPR086W   Sua7p
Schistosoma japonicum Sjp_0303760   ko:K03124 transcription initiation factor TFIIB, putative
Schistosoma japonicum Sjp_0064540   Transcription initiation factor IIB, putative
Schistosoma mansoni Smp_063650.5   transcription initiation factor iib
Schistosoma mansoni Smp_063650.3   transcription initiation factor IIB (TFIIB)
Schmidtea mediterranea mk4.003891.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.005698.01   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.001961.03   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.035816.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.002511.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.013213.02   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.014344.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.047775.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.008667.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.035531.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.011787.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.003212.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.008957.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.010754.00   Putative transcription initiation factor iib
Schmidtea mediterranea mk4.001961.00   Putative transcription initiation factor iib
Toxoplasma gondii TGME49_292000   hypothetical protein
Toxoplasma gondii TGME49_292010   transcription initiation factor IIB
Theileria parva TP02_0202   transcription initiation factor TFIIB, putative
Trichomonas vaginalis TVAG_071030   transcription initiation factor iib, putative

Essentiality

PF3D7_0110800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_W03F9.5 Caenorhabditis elegans embryonic arrest wormbase
CELE_W03F9.5 Caenorhabditis elegans embryonic lethal wormbase
YPR086W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0202900 Plasmodium berghei Slow plasmo
TGME49_292010 Toxoplasma gondii Probably essential sidik
TGME49_292000 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
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_0110800 (Plasmodium falciparum), transcription initiation factor TFIIB, putative
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