Detailed view for LmjF.35.3850

Basic information

TDR Targets ID: 28566
Leishmania major, 30S Ribosomal protein S17-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 10.2636 | Length (AA): 312 | MW (Da): 35960 | 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

PF00366   Ribosomal protein S17

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0006412   translation  

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
105 225 1tmy () 3 118 9.00 0.00000000052 0.05 0.4 -0.4
55 126 4mo2 (B) 151 225 32.00 0.46 0.01 0.321569 1.84
159 288 5cwm (A) 105 227 18.00 0.3 0.25 0.563167 -0.63
217 306 2mcd (A) 8 108 35.00 0.65 0.14 0.168262 1.48

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_128969)

Species Accession Gene Product
Arabidopsis thaliana AT1G49400   protein EMBRYO DEFECTIVE 1129
Arabidopsis thaliana AT3G18880   Nucleic acid-binding, OB-fold-like protein
Arabidopsis thaliana AT1G79850   30S ribosomal protein S17
Candida albicans CaO19.4176   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPS17 (YMR188C) small subunit protein S17
Candida albicans CaO19.11652   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPS17 (YMR188C) small subunit protein S17
Chlamydia trachomatis CT_519   30S ribosomal protein S17
Dictyostelium discoideum DDB_G0277195   ribosomal protein S17, mitochondrial
Escherichia coli b3311   30S ribosomal subunit protein S17
Leishmania braziliensis LbrM.34.3830   30S Ribosomal protein S17-like protein
Leishmania donovani LdBPK_353890.1   30S Ribosomal protein S17-like protein
Leishmania infantum LinJ.35.3890   30S Ribosomal protein S17-like protein
Leishmania major LmjF.35.3850   30S Ribosomal protein S17-like protein
Leishmania mexicana LmxM.34.3850   30S Ribosomal protein S17-like protein
Mycobacterium leprae ML1854c   PROBABLE 30S RIBOSOMAL PROTEIN S17 RPSQ
Mycobacterium tuberculosis Rv0710   30S ribosomal protein S17 RpsQ
Mycobacterium ulcerans MUL_0799   30S ribosomal protein S17
Oryza sativa 4337506   Os04g0691600
Oryza sativa 4345370   Os08g0359600
Saccharomyces cerevisiae YMR188C   mitochondrial 37S ribosomal protein MRPS17
Trypanosoma brucei gambiense Tbg972.9.6740   30S Ribosomal protein S17, putative
Trypanosoma brucei Tb927.9.11300   Mitochondrial ribosomal protein S17
Trypanosoma cruzi TcCLB.508461.420   30S Ribosomal protein S17, putative
Treponema pallidum TP0198   30S ribosomal protein S17
Wolbachia endosymbiont of Brugia malayi Wbm0332   30S ribosomal protein S17

Essentiality

LmjF.35.3850 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2580 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.2580 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.2580 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.2580 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3311 Escherichia coli essential goodall
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
  • 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.
  • 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.

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.35.3850 (Leishmania major), 30S Ribosomal protein S17-like protein
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