Detailed view for Tb927.5.2660

Basic information

TDR Targets ID: 11904
Trypanosoma brucei, NUC130/3NT domain/SDA1, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.6649 | Length (AA): 860 | MW (Da): 97841 | 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

PF05285   SDA1
PF08158   NUC130/3NT domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0019034   viral replication complex  
GO:0005488   binding  
GO:0003723   RNA binding  
GO:0019079   viral genome replication  

Metabolic Pathways

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

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
9 849 1tr2 (A) 22 913 12.00 0 0.7 0.907107 0.99
612 730 5h7u (A) 38 159 30.00 0.51 0.3 0.109372 1.43
613 798 3f57 (A) 1698 1896 11.00 0 0.6 0.285479 -0.45
767 833 5wst (A) 866 932 7.00 0.65 0 0.269307 -1.45

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 Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 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_128086)

Species Accession Gene Product
Arabidopsis thaliana AT4G31520   SDA1 family protein
Arabidopsis thaliana AT1G13160   NUC130/3NT and SDA1 domain-containing protein
Babesia bovis BBOV_I002170   conserved hypothetical protein
Brugia malayi Bm1_52515   SDA1 family protein
Candida albicans CaO19.13969   similar to S. cerevisiae YGR245C
Candida albicans CaO19.6648   similar to S. cerevisiae YGR245C
Caenorhabditis elegans CELE_Y39B6A.14   Protein PRO-3
Cryptosporidium hominis Chro.20363   severe depolymerization of actin; Sda1p
Cryptosporidium parvum cgd2_3430   SDA1-like protein
Dictyostelium discoideum DDB_G0269688   SDA1 domain-containing protein
Drosophila melanogaster Dmel_CG8070   Mystery 45A
Echinococcus granulosus EgrG_001056400   protein sda1
Entamoeba histolytica EHI_009540   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001056400   protein sda1
Giardia lamblia GL50803_16299   Sda1, severe depolymerization of actin
Homo sapiens ENSG00000198301   SDA1 domain containing 1
Leishmania braziliensis LbrM.17.1500   hypothetical protein, conserved
Leishmania donovani LdBPK_171480.1   NUC130/3NT domain/SDA1, putative
Leishmania infantum LinJ.17.1480   hypothetical protein, conserved
Leishmania major LmjF.17.1370   hypothetical protein, conserved
Leishmania mexicana LmxM.17.1370   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_00368   hypothetical protein
Mus musculus ENSMUSG00000029415   SDA1 domain containing 1
Neospora caninum NCLIV_001430   F3F19.18, related
Oryza sativa 4337094   Os04g0630000
Plasmodium berghei PBANKA_0613800   protein SDA1, putative
Plasmodium falciparum PF3D7_0716100   protein SDA1, putative
Plasmodium knowlesi PKNH_0310700   protein SDA1, putative
Plasmodium vivax PVX_000620   protein SDA1, putative
Plasmodium yoelii PY01027   Drosophila melanogaster LD33051p
Saccharomyces cerevisiae YGR245C   Sda1p
Schistosoma japonicum Sjp_0032450   Protein SDA1 homolog, putative
Schistosoma mansoni Smp_176520   hsda/sda1
Schmidtea mediterranea mk4.015334.01   Protein SDA1 homolog
Schmidtea mediterranea mk4.007293.00   Protein SDA1 homolog
Trypanosoma brucei gambiense Tbg972.5.3740   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.2660   NUC130/3NT domain/SDA1, putative
Trypanosoma congolense TcIL3000_5_2710   NUC130/3NT domain/SDA1, putative
Trypanosoma congolense TcIL3000_0_09530   NUC130/3NT domain/SDA1, putative
Trypanosoma cruzi TcCLB.509179.110   NUC130/3NT domain/SDA1, putative
Trypanosoma cruzi TcCLB.507047.140   NUC130/3NT domain/SDA1, putative
Toxoplasma gondii TGME49_294430   hypothetical protein
Theileria parva TP03_0112   hypothetical protein
Trichomonas vaginalis TVAG_349040   conserved hypothetical protein

Essentiality

Tb927.5.2660 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.2660 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.2660 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.5.2660 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.5.2660 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y39B6A.14 Caenorhabditis elegans larval arrest wormbase
CELE_Y39B6A.14 Caenorhabditis elegans slow growth wormbase
YGR245C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0613800 Plasmodium berghei Essential plasmo
TGME49_294430 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) 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: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). 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 procyclic forms . 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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Gene identifier Tb927.5.2660 (Trypanosoma brucei), NUC130/3NT domain/SDA1, putative
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