Detailed view for LmjF.34.0300

Basic information

TDR Targets ID: 24739
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.6515 | Length (AA): 757 | MW (Da): 80593 | 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

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 5 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
96 454 1erj (A) 290 707 15.00 0 0.97 0.52 0.15
120 410 1k8k (C) 9 361 13.00 0.0000071 0.75 0.39 -0.09
249 346 2hes (X) 121 227 31.00 0.12 0.78 0.399858 0.2
249 351 3ow8 (A) 162 265 26.00 0.0059 0.54 0.471463 -0.29
249 583 4j0w (A) 213 464 38.00 0 1 0.532936 0.42

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
Mid 40-60% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 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_128227)

Species Accession Gene Product
Arabidopsis thaliana AT4G05410   WD40-repeats containing protein YAOZHE
Arabidopsis thaliana AT4G21130   U3-55K-like protein 2
Babesia bovis BBOV_III003230   WD domain, G-beta repeat domain containing protein
Brugia malayi Bm1_15070   U3 small nucleolar RNA interacting protein 2
Candida albicans CaO19.2830   U3 small nucleolar RNP-associated protein
Candida albicans CaO19.10348   U3 small nucleolar RNP-associated protein
Caenorhabditis elegans CELE_T02H6.1   Protein T02H6.1, isoform B
Cryptosporidium parvum cgd3_1090   Rrp9p/U3-55K-family snoRNP-associated protein with several WD40 repeats
Dictyostelium discoideum DDB_G0293412   hypothetical protein
Drosophila melanogaster Dmel_CG33505   U3 small nuclear riboprotein factor 55K
Echinococcus granulosus EgrG_000946000   U3 small nucleolar RNA interacting protein 2
Entamoeba histolytica EHI_051880   WD domain containing protein
Entamoeba histolytica EHI_178860   WD domain containing protein
Echinococcus multilocularis EmuJ_000946000   U3 small nucleolar RNA interacting protein 2
Giardia lamblia GL50803_10297   U3 small nucleolar RNA interacting protein, putative
Homo sapiens ENSG00000114767   ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)
Leishmania braziliensis LbrM.13.1360   hypothetical protein, conserved
Leishmania donovani LdBPK_340320.1   hypothetical protein, conserved
Leishmania infantum LinJ.34.0320   hypothetical protein, conserved
Leishmania major LmjF.34.0300   hypothetical protein, conserved
Leishmania mexicana LmxM.33.0300   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_09385   U3 small nucleolar RNA interacting protein 2
Mus musculus ENSMUSG00000041506   RRP9, small subunit (SSU) processome component, homolog (yeast)
Neospora caninum NCLIV_023030   WD-40 repeat protein, related
Oryza sativa 4333495   Os03g0625900
Plasmodium berghei PBANKA_1441500   U3 small nucleolar RNA-interacting protein 2, putative
Plasmodium falciparum PF3D7_1226700   U3 small nucleolar RNA-interacting protein 2, putative
Plasmodium knowlesi PKNH_1446100   U3 small nucleolar RNA-interacting protein 2, putative
Plasmodium vivax PVX_123965   WD domain, G-beta repeat domain containing protein
Plasmodium yoelii PY06717   similar to U3 snoRNP-associated 55-kDa protein
Saccharomyces cerevisiae YPR137W   Rrp9p
Schistosoma japonicum Sjp_0208790   U3 small nucleolar RNA-interacting protein 2, putative
Schistosoma mansoni Smp_144340   hypothetical protein
Schmidtea mediterranea mk4.000357.11  
Trypanosoma brucei gambiense Tbg972.10.3360   hypothetical protein, conserved,predicted WD40 repeat protein
Trypanosoma brucei Tb927.10.2700   predicted WD40 repeat protein
Trypanosoma congolense TcIL3000_10_2330   predicted WD40 repeat protein
Trypanosoma cruzi TcCLB.503959.30   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.506195.250   hypothetical protein, conserved
Toxoplasma gondii TGME49_201710   WD domain, G-beta repeat-containing protein
Theileria parva TP04_0117   zinc finger protein, putative
Trichomonas vaginalis TVAG_139600   WD-repeat protein c2e1p5.05 in chromosome I, putative

Essentiality

LmjF.34.0300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.2700 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.2700 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.2700 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.2700 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T02H6.1 Caenorhabditis elegans slow growth wormbase
YPR137W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1441500 Plasmodium berghei Essential plasmo
TGME49_201710 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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

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.

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.34.0300 (Leishmania major), hypothetical protein, conserved
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