Detailed view for Tb927.7.1910

Basic information

TDR Targets ID: 11958
Trypanosoma brucei, pyridoxal phosphate containing glycine decarboxylase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.4975 | Length (AA): 970 | MW (Da): 106295 | 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

PF01212   Beta-eliminating lyase
PF02347   Glycine cleavage system P-protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0004375   glycine dehydrogenase (decarboxylating) activity  
GO:0019464   glycine decarboxylation via glycine cleavage system  
GO:0003824   catalytic activity  
GO:0030170   pyridoxal phosphate binding  
GO:0016829   lyase activity  
GO:0006544   glycine metabolic process  
GO:0006520   amino acid metabolic process  
GO:0055114   oxidation reduction  
GO:0006546   glycine catabolic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
16 966 4lhd (A) 24 977 51.00 0 1 1.67351 -1.1

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_127334)

Species Accession Gene Product
Arabidopsis thaliana AT2G26080   glycine decarboxylase P-protein 2
Arabidopsis thaliana AT4G33010   glycine dehydrogenase [decarboxylating] 2
Candida albicans CaO19.385   P-subunit of glycine cleavage system
Candida albicans CaO19.8015   P-subunit of glycine cleavage system
Caenorhabditis elegans CELE_R12C12.1   Protein R12C12.1, isoform B
Dictyostelium discoideum DDB_G0287255   glycine cleavage system P-protein
Drosophila melanogaster Dmel_CG3999   CG3999 gene product from transcript CG3999-RA
Escherichia coli b2903   glycine decarboxylase, PLP-dependent, subunit (protein P) of glycine cleavage complex
Homo sapiens ENSG00000178445   glycine dehydrogenase (decarboxylating)
Leishmania braziliensis LbrM.26.0050   glycine dehydrogenase, putative
Leishmania donovani LdBPK_260040.1   glycine dehydrogenase, putative
Leishmania infantum LinJ.26.0040   pyridoxal phosphate containing glycine decarboxylase, putative
Leishmania major LmjF.26.0030   pyridoxal phosphate containing glycine decarboxylase, putative;with=GeneDB:LinJ26_V3.0040
Leishmania mexicana LmxM.26.0030   glycine dehydrogenase, putative
Mycobacterium leprae ML2072c   Probable glycine dehydrogenase GcvB (Glycine decarboxylase) (Glycine cleavage system P-protein)
Mus musculus ENSMUSG00000024827   glycine decarboxylase
Mycobacterium tuberculosis Rv1832   Probable glycine dehydrogenase GcvB (glycine decarboxylase) (glycine cleavage system P-protein)
Mycobacterium ulcerans MUL_3050   glycine dehydrogenase
Oryza sativa 4341516   Os06g0611900
Oryza sativa 4325932   Os01g0711400
Saccharomyces cerevisiae YMR189W   glycine decarboxylase subunit P
Schistosoma japonicum Sjp_0088350   ko:K00282 glycine dehydrogenase subunit 1 [EC1.4.4.2A], putative
Schistosoma japonicum Sjp_0067640   ko:K00282 glycine dehydrogenase subunit 1 [EC1.4.4.2A], putative
Schistosoma mansoni Smp_128690   glycine dehydrogenase (decarboxylating)
Schmidtea mediterranea mk4.003329.04  
Schmidtea mediterranea mk4.003329.02   Glycine dehydrogenase
Schmidtea mediterranea mk4.012677.02   Glycine dehydrogenase
Schmidtea mediterranea mk4.002654.00   Glycine dehydrogenase
Schmidtea mediterranea mk4.002654.01  
Schmidtea mediterranea mk4.009693.02  
Trypanosoma brucei gambiense Tbg972.7.1900   glycine dehydrogenase, putative
Trypanosoma brucei Tb927.7.1910   pyridoxal phosphate containing glycine decarboxylase, putative
Trypanosoma congolense TcIL3000_7_1350   pyridoxal phosphate containing glycine decarboxylase, putative
Trypanosoma cruzi TcCLB.510911.50   glycine dehydrogenase [decarboxylating], putative
Trypanosoma cruzi TcCLB.509163.80   glycine dehydrogenase [decarboxylating], putative

Essentiality

Tb927.7.1910 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.1910 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.1910 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.7.1910 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.1910 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2903 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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) 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.

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 Tb927.7.1910 (Trypanosoma brucei), pyridoxal phosphate containing glycine decarboxylase, putative
Title for this comment
Comment