Detailed view for Tb927.9.12000

Basic information

TDR Targets ID: 20574
Trypanosoma brucei, LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.4234 | Length (AA): 388 | MW (Da): 44399 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 2

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

PF03381   LEM3 (ligand-effect modulator 3) family / CDC50 family

Gene Ontology

Mouse over links to read term descriptions.
GO:0016020   membrane  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 2 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
127 265 2xe5 (A) 99 230 32.00 0.77 0.01 0.404847 1.09
223 350 2qmi (A) 176 303 29.00 0.61 0.31 0.335497 0.9

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 Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic. 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_127172)

Species Accession Gene Product
Arabidopsis thaliana AT1G16360   ligand-effect modulator 3 family protein / CDC50 family protein
Arabidopsis thaliana AT1G79450   ALA-interacting subunit 5
Arabidopsis thaliana AT1G54320   ALA-interacting subunit 3
Arabidopsis thaliana AT3G12740   ALA-interacting subunit 1
Babesia bovis BBOV_IV005490   conserved hypothetical protein
Brugia malayi Bm1_39110   DNA segment, Chr 9, Wayne State University 20, expressed
Candida albicans CaO19.5735   cell division cycle
Candida albicans CaO19.13157   cell division cycle
Caenorhabditis elegans CELE_R08C7.2   Protein CHAT-1, isoform C
Cryptosporidium hominis Chro.50357   hypothetical protein
Cryptosporidium parvum cgd5_360   conserved protein with 2 transmembrane domain
Dictyostelium discoideum DDB_G0276567   hypothetical protein
Drosophila melanogaster Dmel_CG9947   CG9947 gene product from transcript CG9947-RB
Echinococcus granulosus EgrG_000800700   protein of unknown function DUF284 transmembrane eukaryotic
Entamoeba histolytica EHI_142740   hypothetical protein
Echinococcus multilocularis EmuJ_000800700   protein of unknown function DUF284, transmembrane eukaryotic
Giardia lamblia GL50803_15501   CDC50
Homo sapiens ENSG00000112697   transmembrane protein 30A
Leishmania braziliensis LbrM.34.3310   hypothetical protein, conserved
Leishmania donovani LdBPK_353450.1   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Leishmania infantum LinJ.35.3450   hypothetical protein, conserved
Leishmania major LmjF.35.3400   hypothetical protein, conserved
Leishmania mexicana LmxM.34.3400   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03933   transmembrane protein 30A
Mus musculus ENSMUSG00000032328   transmembrane protein 30A
Mus musculus ENSMUSG00000022753   transmembrane protein 30C
Neospora caninum NCLIV_016160   hypothetical protein
Oryza sativa 4339407   Os05g0529900
Oryza sativa 4341775   Os06g0665000
Oryza sativa 4331429   Os03g0120100
Oryza sativa 4328458   Os02g0173800
Plasmodium berghei PBANKA_0617000   LEM3/CDC50 family protein, putative
Plasmodium falciparum PF3D7_0719500   LEM3/CDC50 family protein, putative
Plasmodium knowlesi PKNH_0314900   LEM3/CDC50 family protein, putative
Plasmodium vivax PVX_096345   hypothetical protein, conserved
Plasmodium yoelii PY02459   hypothetical protein
Saccharomyces cerevisiae YCR094W   aminophospholipid translocase regulatory protein CDC50
Schistosoma japonicum Sjp_0305850   Cell cycle control protein 50A, putative
Schistosoma japonicum Sjp_0314720   Cell cycle control protein 50A, putative
Schistosoma japonicum Sjp_0020090   Cell cycle control protein 50A, putative
Schistosoma mansoni Smp_014020.2   cdc50-related
Schistosoma mansoni Smp_014020.1   cdc50-related
Schistosoma mansoni Smp_139920   cdc50-related
Schmidtea mediterranea mk4.000161.09  
Schmidtea mediterranea mk4.000204.08   Cdc50-related
Schmidtea mediterranea mk4.000390.05   Cdc50-related
Schmidtea mediterranea mk4.004426.01   Cdc50-related
Schmidtea mediterranea mk4.000161.07   Cdc50-related
Schmidtea mediterranea mk4.000390.04   Cdc50-related
Schmidtea mediterranea mk4.000390.06   Cdc50-related
Schmidtea mediterranea mk4.000390.09   Cdc50-related
Schmidtea mediterranea mk4.001471.03   Cdc50-related
Schmidtea mediterranea mk4.004426.02  
Trypanosoma brucei gambiense Tbg972.9.7270   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.12000   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Trypanosoma congolense TcIL3000_0_53730   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Trypanosoma congolense TcIL3000_0_41940   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Trypanosoma cruzi TcCLB.507011.180   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Trypanosoma cruzi TcCLB.510665.4   LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
Toxoplasma gondii TGME49_239540   LEM3 (ligand-effect modulator 3) family / CDC50 family protein
Trichomonas vaginalis TVAG_316220   conserved hypothetical protein
Trichomonas vaginalis TVAG_451190   Alkylphosphocholine resistance protein LEM3, putative
Trichomonas vaginalis TVAG_155710   cell division control protein, putative
Trichomonas vaginalis TVAG_288610   Alkylphosphocholine resistance protein LEM3, putative
Trichomonas vaginalis TVAG_043460   cell division control protein, putative
Trichomonas vaginalis TVAG_212490   cell division control protein, putative

Essentiality

Tb927.9.12000 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.3110 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.3110 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.3110 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.3110 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_R08C7.2 Caenorhabditis elegans slow growth wormbase
TGME49_239540 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • 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

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) 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

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 Tb927.9.12000 (Trypanosoma brucei), LEM3 (ligand-effect modulator 3) family / CDC50 family, putative
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