Detailed view for LmjF.35.3540

Basic information

TDR Targets ID: 25960
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 10.2856 | Length (AA): 221 | MW (Da): 24412 | 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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0003723   RNA binding  
GO:0003676   nucleic acid 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
29 220 1tua (A) 1 179 26.00 0 1 1.15 -1.29
29 207 3aev (B) 31 198 36.00 0.00000000014 1 1.13115 -0.39
30 217 1tua (A) 1 176 26.00 0 1 1.23988 -1.24
146 202 1x4m (A) 23 88 19.00 0 0.31 0.422119 -1.3
147 202 2anr (A) 113 177 21.00 0 0.5 0.536594 -1.39

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 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_127464)

Species Accession Gene Product
Arabidopsis thaliana AT3G13230   RNA-binding KH domain-containing protein
Babesia bovis BBOV_IV008880   conserved hypothetical protein
Brugia malayi Bm1_42995   MGC89796 protein
Candida albicans CaO19.7618   similar to S. cerevisiae YOR145C
Caenorhabditis elegans CELE_Y53C12B.2   Protein Y53C12B.2
Cryptosporidium hominis Chro.80193   YOR3513c
Cryptosporidium parvum cgd8_1650   partner of Nob1; Pno1p; Yor145cp like KH domain containing protein
Dictyostelium discoideum DDB_G0287557   RNA-binding protein PNO1
Drosophila melanogaster Dmel_CG11738   lethal (1) G0004
Echinococcus granulosus EgrG_000257400   rRNA processing protein Rrp20
Entamoeba histolytica EHI_065870   RNA-binding protein, putative
Echinococcus multilocularis EmuJ_000257400   rRNA processing protein (Rrp20)
Giardia lamblia GL50803_16718   Partner of Nob1
Homo sapiens ENSG00000115946   partner of NOB1 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.34.3470   hypothetical protein, conserved
Leishmania donovani LdBPK_353590.1   pre-rRNA-processing protein PNO1, putative
Leishmania infantum LinJ.35.3590   hypothetical protein, conserved
Leishmania major LmjF.35.3540   hypothetical protein, conserved
Leishmania mexicana LmxM.34.3540   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_05624   hypothetical protein
Mus musculus ENSMUSG00000020116   partner of NOB1 homolog (S. cerevisiae)
Neospora caninum NCLIV_012590   hypothetical protein, conserved
Oryza sativa 4331393   Os03g0115200
Plasmodium berghei PBANKA_1332500   pre-rRNA-processing protein PNO1, putative
Plasmodium falciparum PF3D7_1469300   pre-rRNA-processing protein PNO1, putative
Plasmodium knowlesi PKNH_1211700   pre-rRNA-processing protein PNO1, putative
Plasmodium vivax PVX_117000   hypothetical protein, conserved
Plasmodium yoelii PY03646   similar to unknown protein
Saccharomyces cerevisiae YOR145C   Pno1p
Schistosoma japonicum Sjp_0306030   ko:K06961 PNO1; partner of NOB1, putative
Schistosoma mansoni Smp_073080.1   hypothetical protein
Schistosoma mansoni Smp_073080.2   rRNA processing protein (Rrp20)
Schmidtea mediterranea mk4.020067.00   Putative rrna processing protein
Trypanosoma brucei gambiense Tbg972.9.7120   hypothetical protein, conserved
Trypanosoma brucei Tb427tmp.211.2960   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.11840   pre-rRNA-processing protein PNO1, putative
Trypanosoma congolense TcIL3000_9_4830   pre-rRNA-processing protein PNO1, putative
Trypanosoma cruzi TcCLB.507005.70   pre-rRNA-processing protein PNO1, putative
Trypanosoma cruzi TcCLB.507011.50   pre-rRNA-processing protein PNO1, putative
Toxoplasma gondii TGME49_220490   pre-rRNA-processing protein PNO1, putative
Theileria parva TP01_0887   hypothetical protein, conserved
Trichomonas vaginalis TVAG_115500   conserved hypothetical protein

Essentiality

LmjF.35.3540 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2960 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.2960 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.2960 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.2960 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y53C12B.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y53C12B.2 Caenorhabditis elegans slow growth wormbase
TGME49_220490 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.

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.35.3540 (Leishmania major), hypothetical protein, conserved
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