Detailed view for LbrM.29.2740

Basic information

TDR Targets ID: 430359
Leishmania braziliensis, hypothetical protein, conserved
Source Database / ID: 

pI: 6.4526 | Length (AA): 1081 | MW (Da): 119971 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

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

PF00233   3'5'-cyclic nucleotide phosphodiesterase
PF01363   FYVE zinc finger

Gene Ontology

Mouse over links to read term descriptions.
GO:0004114   3',5'-cyclic-nucleotide phosphodiesterase activity  
GO:0046872   metal ion binding  
GO:0008081   phosphoric diester hydrolase activity  
GO:0007165   signal transduction  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 6 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
4 73 1joc (A) 1339 1410 33.00 0 0.98 0.341955 0.49
21 68 1wfk (A) 12 60 38.00 0.59 0.79 0.316303 1.15
174 331 5cwj (A) 2 160 19.00 0 0.48 0.443361 -1.51
450 839 4wzi (A) 170 641 26.00 0 1 0.563977 0.32
529 849 3v93 (A) 287 606 43.00 0 1 0.879147 -1.38
549 839 1zkl (A) 151 439 28.00 0 1 0.617395 -0.76

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_154436)

Species Accession Gene Product
Leishmania braziliensis LbrM.29.2740   hypothetical protein, conserved
Leishmania donovani LdBPK_292790.1   hypothetical protein, conserved
Leishmania infantum LinJ.29.2790   hypothetical protein, conserved
Leishmania major LmjF.29.2680   hypothetical protein, conserved
Leishmania mexicana LmxM.08_29.2680   hypothetical protein, conserved
Trypanosoma brucei gambiense Tbg972.3.3220   3, 5-cyclic nucleotide phosphodiesterase, putative
Trypanosoma brucei Tb927.3.3070   3', 5'-cyclic nucleotide phosphodiesterase, putative
Trypanosoma congolense TcIL3000_3_1980   3', 5'-cyclic nucleotide phosphodiesterase, putative
Trypanosoma cruzi TcCLB.506697.20   cyclic nucleotide phosphodiesterase

Essentiality

LbrM.29.2740 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.3070 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.3070 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.3070 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.3.3070 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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
Species Known druggable target Linked compounds Reference
Trypanosoma cruzi cyclic nucleotide phosphodiesterase Compounds References
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

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

Enter your comment

User ()
Gene identifier LbrM.29.2740 (Leishmania braziliensis), hypothetical protein, conserved
Title for this comment
Comment