Detailed view for Rv3460c

Basic information

TDR Targets ID: 7084
Mycobacterium tuberculosis, 30S ribosomal protein S13 RpsM

Source Database / ID:  Tuberculist 

pI: 11.5821 | Length (AA): 124 | MW (Da): 14351 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF00416   Ribosomal protein S13/S18

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0006412   translation  

Metabolic Pathways

Ribosome (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
2 124 2vqe (M) 2 124 62.00 0 1 1.72154 -0.42
13 83 2ynq (A) 308 375 29.00 0.73 0.42 0.985081 -1.26
20 65 1kfv (B) 164 209 28.00 0 0.75 0.798568 -1.05

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 Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_126668)

Species Accession Gene Product
Arabidopsis thaliana AT1G77750   small ribosomal subunit protein S13
Arabidopsis thaliana AT4G09800   40S ribosomal protein S18
Arabidopsis thaliana AT1G34030   40S ribosomal protein S18
Arabidopsis thaliana AT1G22780   40S ribosomal protein S18
Babesia bovis BBOV_IV005450   40S ribosomal protein S18, putative
Brugia malayi Bm1_46915   40S ribosomal protein S18
Candida albicans CaO19.13764   potential mitochondrial ribosomal protein similar to S. cerevisiae SWS2 (YNL081C) putative mitochondrial small subunit protein (
Candida albicans CaO19.7018   likely cytosolic ribosomal protein similar to S. cerevisiae RPS18A (YDR450W) small subunit protein S18A
Candida albicans CaO19.6406   potential mitochondrial ribosomal protein similar to S. cerevisiae SWS2 (YNL081C) putative mitochondrial small subunit protein (
Candida albicans CaO19_7018   hypothetical protein
Caenorhabditis elegans CELE_Y57G11C.16   Protein RPS-18
Cryptosporidium hominis Chro.30283   ribosomal protein S18
Cryptosporidium parvum cgd3_2440   ribosomal protein S18A, rps18ap, HhH domain
Chlamydia trachomatis CT_509   30S ribosomal protein S13
Dictyostelium discoideum DDB_G0276415   40S ribosomal protein S18
Drosophila melanogaster Dmel_CG8900   Ribosomal protein S18
Escherichia coli b3298   30S ribosomal subunit protein S13
Echinococcus granulosus EgrG_000980000   40S ribosomal protein S18
Entamoeba histolytica EHI_031400   ribosomal protein S18, putative
Entamoeba histolytica EHI_086120   ribosomal protein S18, putative
Entamoeba histolytica EHI_009680   ribosomal protein S18, putative
Entamoeba histolytica EHI_086140   Ras guanine nucleotide exchange factor, putative
Echinococcus multilocularis EmuJ_000980000   40S ribosomal protein S18
Giardia lamblia GL50803_15551   Ribosomal protein S18
Homo sapiens ENSG00000231500   ribosomal protein S18
Leishmania braziliensis LbrM.35.1050   40S ribosomal protein S18, putative
Leishmania braziliensis LbrM.35.1060   40S ribosomal protein S18, putative
Leishmania donovani LdBPK_360990.1   40S ribosomal protein S18, putative
Leishmania infantum LinJ.36.1000   40S ribosomal protein S18, putative
Leishmania infantum LinJ.36.0990   40S ribosomal protein S18, putative
Leishmania major LmjF.36.0940   40S ribosomal protein S18, putative
Leishmania major LmjF.36.0930   40S ribosomal protein S18, putative
Leishmania mexicana LmxM.36.0930   40S ribosomal protein S18, putative
Leishmania mexicana LmxM.36.0940   40S ribosomal protein S18, putative
Loa Loa (eye worm) LOAG_07945   40S ribosomal protein S18
Mycobacterium leprae ML1960c   PROBABLE 30S RIBOSOMAL PROTEIN S13 RPSM
Mus musculus ENSMUSG00000008668   ribosomal protein S18
Mus musculus 623505   predicted gene 6436
Mycobacterium tuberculosis Rv3460c   30S ribosomal protein S13 RpsM
Mycobacterium ulcerans MUL_0845   30S ribosomal protein S13
Neospora caninum NCLIV_047630   40S ribosomal protein S18, putative
Oryza sativa 4333848   Os03g0704000
Oryza sativa 6450193   ribosomal protein S13
Oryza sativa 4342526   Os07g0173700
Oryza sativa 4334407   Os03g0794700
Plasmodium berghei PBANKA_0922100   40S ribosomal protein S18, putative
Plasmodium falciparum PF3D7_1126200   40S ribosomal protein S18, putative
Plasmodium knowlesi PKNH_0924100   40S ribosomal protein S18, putative
Plasmodium vivax PVX_091925   40S ribosomal protein S18, putative
Plasmodium yoelii PY07508   ribosomal protein S13/S18
Saccharomyces cerevisiae YDR450W   ribosomal 40S subunit protein S18A
Saccharomyces cerevisiae YML026C   ribosomal 40S subunit protein S18B
Saccharomyces cerevisiae YNL081C   putative mitochondrial 37S ribosomal protein SWS2
Schistosoma japonicum Sjp_0058880   ko:K02964 small subunit ribosomal protein S18e, putative
Schistosoma mansoni Smp_074780   40S ribosomal protein S18
Schmidtea mediterranea mk4.002789.00   40S ribosomal protein S18
Schmidtea mediterranea mk4.005019.05   40S ribosomal protein S18
Schmidtea mediterranea mk4.001291.03   40S ribosomal protein S18
Trypanosoma brucei gambiense Tbg972.10.6520   40S ribosomal protein S18, putative
Trypanosoma brucei gambiense Tbg972.10.6510   40S ribosomal protein S18, putative
Trypanosoma brucei Tb927.10.5330   40S ribosomal protein S18, putative
Trypanosoma brucei Tb11.v5.1060   40S ribosomal protein S18, putative
Trypanosoma brucei Tb927.10.5340   40S ribosomal protein S18, putative
Trypanosoma congolense TcIL3000_10_4490   40S ribosomal protein S18, putative
Trypanosoma congolense TcIL3000_10_4480   40S ribosomal protein S18, putative
Trypanosoma cruzi TcCLB.506679.100   40S ribosomal protein S18, putative
Trypanosoma cruzi TcCLB.506679.94   40S ribosomal protein S18, putative
Toxoplasma gondii TGME49_225080   ribosomal protein RPS18
Treponema pallidum TP0210   30S ribosomal protein S13
Theileria parva TP01_0351   40S ribosomal protein S18, putative
Trichomonas vaginalis TVAG_020480   40S ribosomal protein S18, putative
Trichomonas vaginalis TVAG_065040   30S/40S ribosomal protein, putative
Trichomonas vaginalis TVAG_341090   30S ribosomal protein S13p, putative
Trichomonas vaginalis TVAG_184530   30S ribosomal protein S13, putative
Trichomonas vaginalis TVAG_043810   30S/40S ribosomal protein, putative
Trichomonas vaginalis TVAG_487930   40S ribosomal protein S18, putative
Trichomonas vaginalis TVAG_419040   30S/40S ribosomal protein, putative
Trichomonas vaginalis TVAG_487360   30S ribosomal protein S13p, putative
Wolbachia endosymbiont of Brugia malayi Wbm0320   30S ribosomal protein S13

Essentiality

Rv3460c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.5330 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.5330 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.5330 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.5330 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3298 Escherichia coli essential goodall
CELE_Y57G11C.16 Caenorhabditis elegans sterile wormbase
TGME49_225080 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • 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.

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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Gene identifier Rv3460c (Mycobacterium tuberculosis), 30S ribosomal protein S13 RpsM
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