Detailed view for LmjF.36.2980

Basic information

TDR Targets ID: 24500
Leishmania major, hypothetical protein, conserved,predicted bromodomain protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.2198 | Length (AA): 233 | MW (Da): 26423 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00439   Bromodomain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
2 114 1jm4 (B) 717 830 27.00 0 1 0.8 -0.94
7 109 2fsa (A) 68 170 23.00 0 1 0.97 -2.13
1 118 5c4q (A) 1 118 94.00 0 1 1.71094 -1.72
5 167 4n4f (A) 1083 1297 25.00 0 1 1.00497 -0.41

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 amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_138296)

Species Accession Gene Product
Caenorhabditis elegans CELE_F13C5.2   Protein F13C5.2
Cryptosporidium hominis Chro.80270   bromodomain protein
Leishmania braziliensis LbrM.35.3200   hypothetical protein, conserved,predicted bromodomain protein
Leishmania donovani LdBPK_363130.1   hypothetical protein, conserved
Leishmania infantum LinJ.36.3130   hypothetical protein, conserved,predicted bromodomain protein
Leishmania major LmjF.36.2980   hypothetical protein, conserved,predicted bromodomain protein
Leishmania mexicana LmxM.36.2980   hypothetical protein, conserved,predicted bromodomain protein
Oryza sativa 4331505   Os03g0130800
Trypanosoma brucei gambiense Tbg972.10.9100   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.7420   bromodomain factor 2 protein, putative
Trypanosoma cruzi TcCLB.506553.20   bromodomain factor 2 protein
Trypanosoma cruzi TcCLB.507769.30   hypothetical protein, conserved
Trichomonas vaginalis TVAG_093070   bromodomain-containing protein, putative

Essentiality

LmjF.36.2980 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7420 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.7420 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.7420 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.7420 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F13C5.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_F13C5.2 Caenorhabditis elegans larval arrest wormbase
CELE_F13C5.2 Caenorhabditis elegans larval lethal wormbase
CELE_F13C5.2 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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

  • Lmaj006263AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj006263; Recombinant protein: full-length; Source: L major; hypothetical protein, conserved ;

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 LmjF.36.2980 (Leishmania major), hypothetical protein, conserved,predicted bromodomain protein
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