Detailed view for LmjF.35.3880

Basic information

TDR Targets ID: 23984
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.873 | Length (AA): 444 | MW (Da): 50509 | 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

PF00400   WD domain, G-beta repeat
PF04158   Sof1-like domain

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 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
33 357 1vyh (C) 116 408 21.00 0 1 0.9 0.06
61 357 1got (B) 49 340 22.00 0 1 1.02 -0.73
47 359 3ei3 (B) 118 455 17.00 0 1 0.826555 0.05
83 356 2pbi (B) 78 352 28.00 0 1 0.997417 -0.51
243 356 5k19 (A) 153 289 34.00 0.0000028 0.75 0.407057 -0.36
245 372 3mmy (A) 45 172 28.00 0.00005 1 0.657588 -0.8

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 metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_127890)

Species Accession Gene Product
Arabidopsis thaliana AT4G28450   WD repeat and SOF domain-containing protein 1
Babesia bovis BBOV_IV005130   ribosomal processing protein, putative
Brugia malayi Bm1_10260   gene model 83
Brugia malayi Bm1_28555   Sof1-like domain containing protein
Candida albicans CaO19.5407   small nucleolar ribonucleoprotein
Candida albicans CaO19.12862   small nucleolar ribonucleoprotein
Caenorhabditis elegans CELE_ZK430.7   Protein ZK430.7
Cryptosporidium hominis Chro.80522   hypothetical protein
Cryptosporidium parvum cgd8_4530   ribosomal processing protein, putative
Dictyostelium discoideum DDB_G0276815   hypothetical protein
Drosophila melanogaster Dmel_CG7275   CG7275 gene product from transcript CG7275-RA
Echinococcus granulosus EgrG_000895100   WD repeats and SOF1 domain containing protein
Entamoeba histolytica EHI_083380   hypothetical protein, conserved
Entamoeba histolytica EHI_135930   hypothetical protein, conserved
Entamoeba histolytica EHI_168460   hypothetical protein, conserved
Entamoeba histolytica EHI_085680   WD repeat protein
Echinococcus multilocularis EmuJ_000895100   WD repeats and SOF1 domain containing protein
Giardia lamblia GL50803_8361   SOF1 protein
Homo sapiens ENSG00000164934   DDB1 and CUL4 associated factor 13
Leishmania braziliensis LbrM.34.3860   hypothetical protein, conserved
Leishmania donovani LdBPK_353920.1   WD domain, G-beta repeat/Sof1-like domain containing protein, putative
Leishmania infantum LinJ.35.3920   hypothetical protein, conserved
Leishmania major LmjF.35.3880   hypothetical protein, conserved
Leishmania mexicana LmxM.34.3880   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_01395   WD repeats and SOF1 domain-containing protein
Mus musculus ENSMUSG00000022300   DDB1 and CUL4 associated factor 13
Neospora caninum NCLIV_033200   hypothetical protein
Oryza sativa 4326362   Os01g0238900
Plasmodium berghei PBANKA_1006800   protein SOF1, putative
Plasmodium falciparum PF3D7_0409200   protein SOF1, putative
Plasmodium knowlesi PKNH_0307200   protein SOF1, putative
Plasmodium vivax PVX_000785   ribosomal processing protein, putative
Plasmodium yoelii PY04096   putative ribosomal processing protein
Saccharomyces cerevisiae YLL011W   Sof1p
Schistosoma japonicum Sjp_0080990   WD repeat and SOF domain-containing protein 1, putative
Schistosoma mansoni Smp_134060   U3 small nucleolar rna (U3 snorna) associated protein
Schmidtea mediterranea mk4.002142.06   DDB1- and CUL4-associated factor 13
Schmidtea mediterranea mk4.002370.01   DDB1- and CUL4-associated factor 13
Trypanosoma brucei gambiense Tbg972.9.6710   WD40 repeat protein, predicted
Trypanosoma brucei Tb927.9.11250   predicted WD40 repeat protein
Trypanosoma congolense TcIL3000_9_4630   predicted WD40 repeat protein
Trypanosoma cruzi TcCLB.508461.390   hypothetical protein, conserved
Toxoplasma gondii TGME49_233410   Sof1 family domain-containing protein
Theileria parva TP01_0231   ribosomal processing protein, putative
Trichomonas vaginalis TVAG_497110   U3 small nucleolar RNA (U3 snoRNA) associated protein, putative

Essentiality

LmjF.35.3880 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2550 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.2550 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.2550 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.2550 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK430.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK430.7 Caenorhabditis elegans larval arrest wormbase
CELE_ZK430.7 Caenorhabditis elegans slow growth wormbase
YLL011W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1006800 Plasmodium berghei Essential plasmo
TGME49_233410 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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

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.35.3880 (Leishmania major), hypothetical protein, conserved
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