Detailed view for Tb927.8.6540

Basic information

TDR Targets ID: 14255
Trypanosoma brucei, TFIIH basal transcription factor subunit
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.2193 | Length (AA): 351 | MW (Da): 37989 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF04056   Ssl1-like

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0005675   holo TFIIH complex  
GO:0003674   molecular_function  
GO:0000439   core TFIIH complex  
GO:0008270   zinc ion binding  
GO:0006350   transcription  
GO:0006289   nucleotide-excision repair  
GO:0006281   DNA repair  
GO:0045449   regulation of transcription  

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
4 209 2x5n (A) 6 192 23.00 0 1 0.740695 -0.23
4 204 4wfq (A) 126 307 25.00 0 1 0.85145 -0.88
299 347 1weo (A) 14 64 29.00 0 0.41 0.363401 0.57
312 343 2eoi (A) 3 34 16.00 0.00012 0.04 0.100868 1.08

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 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_127799)

Species Accession Gene Product
Arabidopsis thaliana AT1G05055   transcription initiation factor TFIIH subunit H2
Babesia bovis BBOV_IV001810   transcriptional factor 2 subunit
Brugia malayi Bm1_30170   TFIIH basal transcription factor complex p44 subunit, putative
Candida albicans CaO19.1457   subunit of transcription factor TF2H
Candida albicans CaO19.9032   subunit of transcription factor TF2H
Caenorhabditis elegans CELE_T16H12.4   Protein T16H12.4
Cryptosporidium hominis Chro.30353   hypothetical protein
Cryptosporidium parvum cgd3_3110   transcription factor TFIIH with a vWA domain
Dictyostelium discoideum DDB_G0272362   TFIIH subunit
Drosophila melanogaster Dmel_CG11115   Suppressor of Stem-Loop mutation ortholog (S. cerevisiae)
Echinococcus granulosus EgrG_000495100   TFIIH C1 C terminal
Entamoeba histolytica EHI_182880   TFIIH basal transcription factor complex subunit, putative
Echinococcus multilocularis EmuJ_000495100   TFIIH C1, C terminal
Giardia lamblia GL50803_15000   TFIIH P44
Homo sapiens ENSG00000183474   GTF2H2 family member C
Homo sapiens ENSG00000145736   general transcription factor IIH, polypeptide 2, 44kDa
Homo sapiens 730394   GTF2H2 family member C, copy 2
Leishmania braziliensis LbrM.24.1740   hypothetical protein, conserved
Leishmania donovani LdBPK_241750.1   Ssl1-like, putative
Leishmania infantum LinJ.24.1750   hypothetical protein, conserved
Leishmania major LmjF.24.1680   hypothetical protein, conserved
Leishmania mexicana LmxM.24.1680   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_05169   hypothetical protein
Mus musculus ENSMUSG00000021639   general transcription factor II H, polypeptide 2
Neospora caninum NCLIV_001790   general transcription factor IIH polypeptide 2, putative
Oryza sativa 4336358   Os04g0508900
Onchocerca volvulus OVOC12467   General transcription factor IIH subunit 2 homolog
Plasmodium berghei PBANKA_1413400   general transcription factor IIH subunit 2, putative
Plasmodium falciparum PF3D7_1314900   general transcription factor IIH subunit 2
Plasmodium knowlesi PKNH_1415600   general transcription factor IIH subunit 2, putative
Plasmodium vivax PVX_122565   general transcription factor IIH subunit 2, putative
Plasmodium yoelii PY06921   W43325 comes from this gene., putative
Saccharomyces cerevisiae YLR005W   TFIIH/NER complex subunit SSL1
Schistosoma japonicum Sjp_0310460   ko:K03142 transcription initiation factor TFIIH subunit H2, putative
Schistosoma japonicum Sjp_0219370   General transcription factor IIH subunit 2, putative
Schistosoma mansoni Smp_136520   btf
Schmidtea mediterranea mk4.001077.02   General transcription factor IIH subunit 2
Trypanosoma brucei gambiense Tbg972.8.6640   DNA repair and transcription factor protein, putative
Trypanosoma brucei Tb927.8.6540   TFIIH basal transcription factor subunit
Trypanosoma congolense TcIL3000_8_6380   DNA repair and transcription factor protein, putative
Trypanosoma cruzi TcCLB.511907.300   transcription factor II H complex, SSL1 subunit, putative
Toxoplasma gondii TGME49_294920   general transcription factor IIH polypeptide 2 GTF2H2
Theileria parva TP03_0481   hypothetical protein, conserved
Trichomonas vaginalis TVAG_290240   ssl1, putative
Trichomonas vaginalis TVAG_100760   ssl1, putative

Essentiality

Tb927.8.6540 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.6540 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.6540 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.6540 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.6540 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T16H12.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_T16H12.4 Caenorhabditis elegans larval lethal wormbase
CELE_T16H12.4 Caenorhabditis elegans slow growth wormbase
YLR005W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1413400 Plasmodium berghei Essential plasmo
TGME49_294920 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

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User comments

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Gene identifier Tb927.8.6540 (Trypanosoma brucei), TFIIH basal transcription factor subunit
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