Detailed view for LmjF.34.4550

Basic information

TDR Targets ID: 28081
Leishmania major, cell differentiation protein-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.3212 | Length (AA): 360 | MW (Da): 41113 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF04078   Cell differentiation family, Rcd1-like

Gene Ontology

Mouse over links to read term descriptions.
GO:0030014   CCR4-NOT complex  
GO:0005488   binding  
GO:0006402   mRNA catabolic process  

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 3 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
17 70 4dmu (A) 4 226 28.00 0.63 0.03 0.2303 1.25
28 60 4dmu (A) 11 126 21.00 0 0.03 0.372067 -0.9
74 346 4cru (B) 18 285 49.00 0 1 1.54363 -2.23

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 60-80% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile amastigotes. 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_128041)

Species Accession Gene Product
Arabidopsis thaliana AT5G12980   Cell differentiation, Rcd1-like protein
Arabidopsis thaliana AT3G20800   cell differentiation, Rcd1-like protein
Babesia bovis BBOV_III004860   cell differentiation family protein
Brugia malayi Bm1_45760   Cell differentiation protein rcd1
Candida albicans CaO19.7198   similar to S. cerevisiae CAF40 (YNL288W) Rcd1-like factor associated with the CCR4-NOT transcription factor complex
Candida albicans CaO19_7198   hypothetical protein
Caenorhabditis elegans CELE_C26E6.3   Protein NTL-9
Cryptosporidium hominis Chro.80511   cell differentiation protein rcd1
Cryptosporidium parvum cgd8_4460   cell differentiation protein rcd1, putative
Dictyostelium discoideum DDB_G0269778   cell differentiation family, Rcd1-like protein
Drosophila melanogaster Dmel_CG14213   Required for cell differentiation 1 ortholog
Echinococcus granulosus EgrG_000966200   cell differentiation protein rcd1
Entamoeba histolytica EHI_093570   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000966200   cell differentiation protein rcd1
Homo sapiens ENSG00000144580   RCD1 required for cell differentiation1 homolog (S. pombe)
Leishmania braziliensis LbrM.20.4010   cell differentiation protein-like protein
Leishmania donovani LdBPK_344180.1   cell differentiation protein-like protein
Leishmania infantum LinJ.34.4180   cell differentiation protein-like protein
Leishmania major LmjF.34.4550   cell differentiation protein-like protein
Leishmania mexicana LmxM.33.4550   cell differentiation protein-like protein
Mus musculus ENSMUSG00000026174   rcd1 (required for cell differentiation) homolog 1 (S. pombe)
Neospora caninum NCLIV_027510   hypothetical protein
Oryza sativa 4343622   Os07g0565200
Oryza sativa 4336974   Os04g0613400
Plasmodium berghei PBANKA_1107200   cell differentiation protein, putative
Plasmodium falciparum PF3D7_0507600   cell differentiation protein, putative
Plasmodium knowlesi PKNH_1026000   cell differentiation protein, putative
Plasmodium vivax PVX_097940   cell differentiation protein rcd1, putative
Plasmodium yoelii PY05128   hypothetical protein
Saccharomyces cerevisiae YNL288W   CCR4-NOT core subunit CAF40
Schistosoma japonicum Sjp_0076130   Cell differentiation protein RCD1 homolog, putative
Schistosoma japonicum Sjp_0311130   Cell differentiation protein RCD1 homolog, putative
Schmidtea mediterranea mk4.001835.02   Cell differentiation protein RCD1 homolog
Trypanosoma brucei gambiense Tbg972.4.140   cell differentiation protein, putative
Trypanosoma brucei Tb927.4.410   CAF 40
Trypanosoma congolense TcIL3000_4_90   cell differentiation protein, putative
Trypanosoma cruzi TcCLB.510689.50   cell differentiation protein, putative
Trypanosoma cruzi TcCLB.507873.20   cell differentiation protein, putative
Toxoplasma gondii TGME49_258980   hypothetical protein
Theileria parva TP02_0463   hypothetical protein
Trichomonas vaginalis TVAG_149000   protein CAF40, putative

Essentiality

LmjF.34.4550 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.410 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.410 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.410 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.4.410 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C26E6.3 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_1107200 Plasmodium berghei Essential plasmo
TGME49_258980 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
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

No literature references available for this target.

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User comments

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Gene identifier LmjF.34.4550 (Leishmania major), cell differentiation protein-like protein
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