Detailed view for Tb927.8.6480

Basic information

TDR Targets ID: 15856
Trypanosoma brucei, folate-binding protein YgfZ, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.4386 | Length (AA): 339 | MW (Da): 36943 | Paralog Number: 0

Signal peptide: Y | 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

PF01571   Aminomethyltransferase folate-binding domain
PF08669   Glycine cleavage T-protein C-terminal barrel domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0019464   glycine decarboxylation via glycine cleavage system  
GO:0005737   cytoplasm  
GO:0005576   extracellular region  
GO:0005515   protein binding  
GO:0004047   aminomethyltransferase activity  
GO:0006546   glycine catabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
6 325 3gir (A) 59 364 16.00 0 0.95 1.10505 0.24
7 323 3ttg (A) 21 328 21.00 0 1 1.1004 0.12
7 325 1wos (A) 48 352 18.00 0 0.97 1.0603 0.05
7 238 1vly (A) 24 237 25.00 0.0013 1 0.904166 -0.08
9 299 3ttg (A) 23 310 28.00 0.00000027 0.79 0.874207 0.65

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, 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_128882)

Species Accession Gene Product
Arabidopsis thaliana AT4G12130   mitochondrial-type protein COG0354
Babesia bovis BBOV_I001650   conserved hypothetical protein
Brugia malayi Bm1_00450   aminomethyltransferase
Candida albicans CaO19.318   similar to S. cerevisiae CAF17 (YJR122W) putative CCR4 transcriptional complex associated factor
Candida albicans CaO19.7950   similar to S. cerevisiae CAF17 (YJR122W) putative CCR4 transcriptional complex associated factor
Caenorhabditis elegans CELE_F39H2.3   Protein F39H2.3
Dictyostelium discoideum DDB_G0285011   hypothetical protein
Drosophila melanogaster Dmel_CG8043   CG8043 gene product from transcript CG8043-RA
Echinococcus granulosus EgrG_000187600   protein of unknown function DUF1279
Echinococcus multilocularis EmuJ_000187600   protein of unknown function DUF1279
Homo sapiens ENSG00000181873   IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)
Leishmania braziliensis LbrM.24.1800   hypothetical protein, conserved
Leishmania donovani LdBPK_241810.1   folate-binding protein YgfZ, putative
Leishmania infantum LinJ.24.1810   hypothetical protein, conserved
Leishmania major LmjF.24.1740   hypothetical protein, conserved
Leishmania mexicana LmxM.24.1740   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_15192   aminomethyltransferase
Loa Loa (eye worm) LOAG_07189   hypothetical protein
Loa Loa (eye worm) LOAG_11663   hypothetical protein
Oryza sativa 4340033   Os06g0134800
Onchocerca volvulus OVOC7263   Putative transferase CAF17, mitochondrial
Saccharomyces cerevisiae YJR122W   Iba57p
Schistosoma japonicum Sjp_0302650   ko:K06980 Glycine cleavage T protein, putative
Schistosoma mansoni Smp_170950   hypothetical protein
Schmidtea mediterranea mk4.000208.00   Putative transferase CAF17, mitochondrial
Trypanosoma brucei gambiense Tbg972.8.6560   hypothetical protein, conserved
Trypanosoma brucei Tb927.8.6480   folate-binding protein YgfZ, putative
Trypanosoma cruzi TcCLB.506801.110   folate-binding protein YgfZ, putative
Trypanosoma cruzi TcCLB.511907.230   folate-binding protein YgfZ, putative
Wolbachia endosymbiont of Brugia malayi Wbm0348   glycine cleavage system protein T

Essentiality

Tb927.8.6480 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.6480 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.6480 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.6480 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.6480 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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) 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Tb927.8.6480 (Trypanosoma brucei), folate-binding protein YgfZ, putative
Title for this comment
Comment