Detailed view for Tb927.11.9170
Basic information
Trypanosoma brucei, DNA topoisomerase III, putative
Source Database / ID: TriTrypDB GeneDB
pI: 8.2049 |
Length (AA): 841 |
MW (Da): 93689 |
Paralog Number:
0
Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0
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
Network
Gene Ontology
GO:0003677 DNA binding
GO:0003676 nucleic acid binding
GO:0003917 DNA topoisomerase type I activity
GO:0003916 DNA topoisomerase activity
GO:0006304 DNA modification
GO:0006268 DNA unwinding during replication
GO:0006265 DNA topological change
GO:0006259 DNA metabolic process
Metabolic Pathways
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 |
|---|---|---|---|---|---|---|---|---|---|
| 2 | 605 | 4cgy (A) | 33 | 639 | 35.00 | 0 | 1 | 1.20289 | -0.73 |
| 2 | 602 | 5gvc (A) | 1 | 612 | 51.00 | 0 | 1 | 1.38803 | -0.9 |
| 584 | 670 | 1a6a (B) | 29 | 121 | 33.00 | 0.83 | 0.06 | 0.0678483 | 1.75 |
| 810 | 840 | 1x6e (A) | 32 | 63 | 10.00 | 0.66 | 0 | 0.170261 | -0.96 |
Help me make sense of these data.
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:
Expression
| Upregulation Percent | Ranking | Stage | Dataset |
|---|---|---|---|
| Upper 80-100% percentile | Procyclic, Bloodstream Form. | Siegel TN |
-
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_129147)
| Species | Accession | Gene Product |
|---|---|---|
| Arabidopsis thaliana | AT2G32000 | DNA topoisomerase, type IA, core |
| Babesia bovis | BBOV_II000360 | DNA topoisomerase, putative |
| Brugia malayi | Bm1_24915 | DNA topoisomerase III beta-1 |
| Caenorhabditis elegans | CELE_Y48C3A.14 | Protein Y48C3A.14, isoform D |
| Cryptosporidium hominis | Chro.60278 | DNA topoisomerase III beta-1 |
| Cryptosporidium parvum | cgd6_2390 | DNA topoisomerase III beta-1, putative |
| Drosophila melanogaster | Dmel_CG3458 | Topoisomerase 3beta |
| Echinococcus granulosus | EgrG_000718300 | DNA topoisomerase 3 beta 1 |
| Entamoeba histolytica | EHI_042880 | DNA topoisomerase III, putative |
| Echinococcus multilocularis | EmuJ_000718300 | DNA topoisomerase 3 beta 1 |
| Giardia lamblia | GL50803_15190 | DNA topoisomerase III |
| Homo sapiens | ENSG00000100038 | topoisomerase (DNA) III beta |
| Leishmania braziliensis | LbrM.28.1950 | DNA topoisomerase III, putative |
| Leishmania donovani | LdBPK_281900.1 | DNA topoisomerase III, putative |
| Leishmania infantum | LinJ.28.1900 | DNA topoisomerase III, putative |
| Leishmania major | LmjF.28.1780 | DNA topoisomerase III, putative |
| Leishmania mexicana | LmxM.28.1780 | DNA topoisomerase III, putative |
| Loa Loa (eye worm) | LOAG_06591 | DNA topoisomerase III beta-1 |
| Mus musculus | ENSMUSG00000022779 | topoisomerase (DNA) III beta |
| Neospora caninum | NCLIV_040590 | DNA topoisomerase (EC 5.99.1.2), related |
| Oryza sativa | 4347482 | Os09g0500600 |
| Onchocerca volvulus | OVOC10269 |
|
| Schistosoma japonicum | Sjp_0097620 | expressed protein |
| Schistosoma japonicum | Sjp_0045500 | ko:K03165 DNA topoisomerase III, putative |
| Schistosoma mansoni | Smp_169790 | prokaryotic DNA topoisomerase |
| Schmidtea mediterranea | mk4.000116.05 | DNA topoisomerase 3-beta-1 |
| Schmidtea mediterranea | mk4.000116.04 | |
| Trypanosoma brucei gambiense | Tbg972.11.10250 | DNA topoisomerase III, putative |
| Trypanosoma brucei | Tb927.11.9170 | DNA topoisomerase III, putative |
| Trypanosoma congolense | TcIL3000.11.9530 | DNA topoisomerase III, putative |
| Trypanosoma cruzi | TcCLB.510901.100 | DNA topoisomerase III, putative |
Essentiality
| Gene/Ortholog | Organism | Phenotype | Source Study |
|---|---|---|---|
| Tb11.01.0910 this record | Trypanosoma brucei | no significant loss or gain of fitness in bloodstream forms (3 days) | alsford |
| Tb11.01.0910 this record | Trypanosoma brucei | significant gain of fitness in bloodstream forms (6 days) | alsford |
| Tb11.01.0910 this record | Trypanosoma brucei | no significant loss or gain of fitness in procyclic forms | alsford |
| Tb11.01.0910 this record | Trypanosoma brucei | significant loss of fitness in differentiation of procyclic to bloodstream forms | alsford |
-
wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170 -
blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930 -
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 -
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 -
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 -
yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
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 3 days). | References: | 21363968 | |
| cell proliferation (GO:0008283) | increased (PATO:0000470) | 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: | increased cell proliferation (significant 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 procyclic forms . | References: | 21363968 | |
| cell proliferation (GO:0008283) | decreased (PATO:0000468) | procyclic (PLO:0034) | inferred from RNAi experiment (ECO:0000019) | No drug identifiers listed for this gene. | ||
| Annotator: | fernan@iib.unsam.edu.ar. | Comment: | decreased cell proliferation (significant loss 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
Associated compounds / Druggability
Druggability index (range: 0 to 1): 0.6
Known modulators for this target
Predicted associations
By orthology with druggable targets
| Species | Known druggable target | Linked compounds | Reference |
|---|---|---|---|
| Bacillus subtilis (strain 168) | DNA topoisomerase III | Compounds | References |
By sequence similarity to non orthologous druggable targets
Obtained from network model
Ranking Plot
Putative Drugs List
Assayability
Assay information
Reagent availability
Bibliographic References
22 literature references were collected for this gene.