Detailed view for Tb927.11.5260

Basic information

TDR Targets ID: 20400
Trypanosoma brucei, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.7262 | Length (AA): 968 | MW (Da): 105175 | 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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0006338   chromatin remodeling  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 8 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
75 241 2jzc (A) 27 171 32.00 0.028 0.52 -0.0134009 1.93
157 687 3mwy (W) 353 913 20.00 0 1 0.654221 0.54
176 639 1z63 (A) 440 883 31.00 0 1 0.684735 0.5
471 608 4db2 (A) 346 478 16.00 0 0.46 0.341809 -0.52
477 634 2hjv (A) 223 368 14.00 0 0.89 0.331492 -0.42
626 967 4k6j (A) 652 1008 10.00 0 0.02 0.432771 -0.21
665 794 4d7u (A) 75 210 15.00 0 0.02 0.245536 -0.26
686 881 1ddl (A) 8 185 18.00 0 0.16 0.182789 0.35

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
Mid 40-60% 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_128295)

Species Accession Gene Product
Arabidopsis thaliana AT1G48310   chromatin remodeling factor18
Babesia bovis BBOV_III009710   helicase conserved C-terminal domain containing protein
Brugia malayi Bm1_47190   Helicase conserved C-terminal domain containing protein
Caenorhabditis elegans CELE_C16A3.1   Protein C16A3.1, isoform C
Cryptosporidium hominis Chro.50381   DNA helicase
Cryptosporidium parvum cgd5_150   HARP like SWI/SNF ATpase
Dictyostelium discoideum DDB_G0274965   CHR group protein
Dictyostelium discoideum DDB_G0281559   CHR group protein
Drosophila melanogaster Dmel_CG3753   CG3753 gene product from transcript CG3753-RA
Echinococcus granulosus EgrG_001166900   SWI:SNF matrix associated
Entamoeba histolytica EHI_141120   helicase, putative
Echinococcus multilocularis EmuJ_001166900   SWI:SNF matrix associated
Homo sapiens ENSG00000138375   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
Homo sapiens ENSG00000121988   zinc finger, RAN-binding domain containing 3
Leishmania braziliensis LbrM.24.0620   DNA helicase, putative
Leishmania donovani LdBPK_240620.1   SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Leishmania infantum LinJ.24.0620   DNA helicase, putative
Leishmania major LmjF.24.0610   DNA helicase, putative
Leishmania mexicana LmxM.24.0610   DNA helicase, putative
Loa Loa (eye worm) LOAG_14827   hypothetical protein
Loa Loa (eye worm) LOAG_11737   hypothetical protein
Mus musculus ENSMUSG00000036086   zinc finger, RAN-binding domain containing 3
Mus musculus 54380   SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
Neospora caninum NCLIV_068530   SNF2 family N-terminal domain-containing protein, putative
Oryza sativa 4344031   Os07g0636200
Onchocerca volvulus OVOC7632  
Plasmodium berghei PBANKA_1133800   DNA helicase, putative
Plasmodium falciparum PF3D7_1357500   DNA helicase, putative
Plasmodium knowlesi PKNH_1114000   DNA helicase, putative
Plasmodium vivax PVX_114850   helicase, putative
Plasmodium yoelii PY05882   hypothetical protein
Schistosoma japonicum Sjp_0019080   26S proteasome non-ATPase regulatory subunit 14, putative
Schistosoma mansoni Smp_131000   harp (smarcal1)-related
Schmidtea mediterranea mk4.003006.02   Putative SMARCAL1-like protein
Schmidtea mediterranea mk4.018178.00   Putative SMARCAL1-like protein
Trypanosoma brucei gambiense Tbg972.11.5940   SNF2 DNA repair protein, putative,SNF2 family protein
Trypanosoma brucei Tb927.11.5260   SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Trypanosoma congolense TcIL3000.11.5500   SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Trypanosoma congolense TcIL3000.11.5480   SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Trypanosoma cruzi TcCLB.503981.90   SNF2 family protein
Trypanosoma cruzi TcCLB.504131.150   SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
Trypanosoma cruzi TcCLB.504125.10   SNF2 family protein
Toxoplasma gondii TGME49_277070   SWI2/SNF2-containing protein
Theileria parva TP04_0886   DNA helicase, putative
Trichomonas vaginalis TVAG_191440   helicase, putative

Essentiality

Tb927.11.5260 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.2930 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.2930 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.2930 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.2930 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_1133800 Plasmodium berghei Dispensable plasmo
TGME49_277070 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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) 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 Tb927.11.5260 (Trypanosoma brucei), SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein, putative
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