Detailed view for Bm1_21850

Basic information

TDR Targets ID: 234785
Brugia malayi, SH2 domain containing protein
Source Database / ID:  GenBank

pI: 4.6485 | Length (AA): 1512 | MW (Da): 176623 | 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

PF00575   S1 RNA binding domain
PF14633   SH2 domain
PF14635   Helix-hairpin-helix motif
PF14639   Holliday-junction resolvase-like of SPT6
PF14641   Helix-turn-helix DNA-binding domain of SPT6
PF14878   Death-like domain of SPT6

Gene Ontology

Mouse over links to read term descriptions.
GO:0032784   regulation of RNA elongation  
GO:0006139   nucleobase, nucleoside, nucleotide and nucleic acid metabolic process  
GO:0000991   GO:transcription factor activity, core RNA polymerase II binding  

GO:0005515   protein binding  
GO:0003723   RNA binding  
GO:0003711   transcription elongation regulator activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0006357   regulation of transcription from RNA polymerase II promoter  

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
2 88 3q8t (A) 175 261 9.00 0.98 0 0.25844 -1.4
20 250 3fby (A) 269 525 29.00 0.77 0.05 0.0701778 2.06
292 1253 3psi (A) 314 1197 19.00 0 1 0.581443 0.99
1188 1246 2k4k (A) 6 62 12.00 0.57 0.05 0.224921 -1.2
1305 1493 3psk (A) 1250 1436 28.00 0 1 0.4832 -0.66
1307 1456 3pjp (A) 1251 1396 34.00 0 1 0.541606 -0.34
1415 1498 2hdv (A) 520 618 21.00 0.055 0.55 0.314456 -1.13
1420 1512 4roj (A) 671 769 13.00 0.000045 0.28 0.245408 -1.15

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128378)

Species Accession Gene Product
Arabidopsis thaliana AT1G63210   transcription elongation factor SPT6
Arabidopsis thaliana AT1G65440   transcription elongation factor SPT6-like protein
Babesia bovis BBOV_III001880   conserved hypothetical protein
Brugia malayi Bm1_21850   SH2 domain containing protein
Candida albicans CaO19_7136   hypothetical protein
Candida albicans CaO19.7136   chromatin structure, gene expression
Caenorhabditis elegans CELE_T04A8.14   Protein EMB-5
Cryptosporidium hominis Chro.60604   hypothetical protein
Cryptosporidium parvum cgd6_5250   transcription elongation factor, SPT6-like
Dictyostelium discoideum DDB_G0272354   SH2 domain-containing protein
Dictyostelium discoideum DDB_G0270920   hypothetical protein
Drosophila melanogaster Dmel_CG12225   CG12225 gene product from transcript CG12225-RA
Echinococcus granulosus EgrG_000815600   transcription elongation factor spt6
Echinococcus granulosus EgrG_000815400   transcription elongation factor spt6
Entamoeba histolytica EHI_092290   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000815400   transcription elongation factor spt6
Echinococcus multilocularis EmuJ_000815600   transcription elongation factor spt6
Homo sapiens ENSG00000109111   suppressor of Ty 6 homolog (S. cerevisiae)
Loa Loa (eye worm) LOAG_08467   SH2 domain-containing protein
Mus musculus ENSMUSG00000002052   suppressor of Ty 6
Neospora caninum NCLIV_053360   hypothetical protein, conserved
Oryza sativa 4339194   Os05g0494900
Plasmodium berghei PBANKA_1036000   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1406200   conserved Plasmodium protein, unknown function
Plasmodium knowlesi PKNH_1351900   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_086120   hypothetical protein, conserved
Plasmodium yoelii PY03219   Arabidopsis thaliana BRAHMA ortholog
Plasmodium yoelii PY03867   GAF domain protein
Plasmodium yoelii PY04114   KED, putative
Saccharomyces cerevisiae YGR116W   Spt6p
Schistosoma japonicum Sjp_0057480   Transcription elongation factor SPT6, putative
Schistosoma japonicum Sjp_0057500   Transcription elongation factor SPT6, putative
Schistosoma japonicum Sjp_0312560   Transcription elongation factor SPT6, putative
Schistosoma japonicum Sjp_0305530   Transcription elongation factor SPT6, putative
Schistosoma japonicum Sjp_0057490   Transcription elongation factor SPT6, putative
Schistosoma japonicum Sjp_0057470   expressed protein
Schistosoma mansoni Smp_180420   suppressor of ty
Schmidtea mediterranea mk4.000796.00   Transcription elongation factor SPT6
Schmidtea mediterranea mk4.000393.13   Transcription elongation factor SPT6
Schmidtea mediterranea mk4.000393.12   Suppressor of Ty 6 homolog
Toxoplasma gondii TGME49_308890   transcription elongation factor SPT6
Theileria parva TP03_0651   hypothetical protein
Trichomonas vaginalis TVAG_145250   suppressor of ty, putative

Essentiality

Bm1_21850 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_T04A8.14 Caenorhabditis elegans embryonic lethal wormbase
CELE_T04A8.14 Caenorhabditis elegans larval arrest wormbase
CELE_T04A8.14 Caenorhabditis elegans slow growth wormbase
CELE_T04A8.14 Caenorhabditis elegans sterile wormbase
YGR116W Saccharomyces cerevisiae inviable yeastgenome
TGME49_308890 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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.

User comments

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Gene identifier Bm1_21850 (Brugia malayi), SH2 domain containing protein
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