Detailed view for Rv1630

Basic information

TDR Targets ID: 7072
Mycobacterium tuberculosis, 30S ribosomal protein S1 RpsA
Source Database / ID:  Tuberculist 

pI: 4.5603 | Length (AA): 481 | MW (Da): 53202 | 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

PF00575   S1 RNA binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
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 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
4 76 5lm7 (A) 106 175 30.00 0.069 0.24 0.354067 0.69
5 185 5lm7 (A) 107 275 27.00 0.024 0.62 0.496999 0.7
20 196 4q7j (D) 3 179 41.00 0 1 0.746683 0.9
280 441 4nnh (A) 280 441 92.00 0 1 1.4015 -0.97

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:

PDB tag
  • 4NNG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4NNI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4NNK:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. hasan
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_126915)

Species Accession Gene Product
Arabidopsis thaliana AT5G30510   small subunit ribosomal protein S1
Arabidopsis thaliana AT3G11964   protein ribosomal RNA processing 5
Babesia bovis BBOV_IV005070   conserved hypothetical protein
Brugia malayi Bm1_01745   S1 RNA binding domain containing protein
Candida albicans CaO19.1578   processing of pre-rRNA to 18S and 5.8S rRNA
Candida albicans CaO19.9151   processing of pre-rRNA to 18S and 5.8S rRNA
Caenorhabditis elegans CELE_C16A3.3   Protein LET-716
Cryptosporidium hominis Chro.80242   rrp5 protein
Cryptosporidium parvum cgd8_2050   RRP5 like protein involved in rRNA biogenesis with 7 S1 domains and 5 HAT repeats
Chlamydia trachomatis CT_098   30S ribosomal protein S1
Dictyostelium discoideum DDB_G0290181   HAT repeat-containing protein
Drosophila melanogaster Dmel_CG5728   CG5728 gene product from transcript CG5728-RA
Escherichia coli b0911   30S ribosomal subunit protein S1
Echinococcus granulosus EgrG_000014400   programmed cell death protein 11
Echinococcus granulosus EgrG_001068100   protein rrp5
Entamoeba histolytica EHI_033670   S1 RNA binding domain-containing protein
Entamoeba histolytica EHI_160440   rRNA biogenesis protein RRP5, putative
Entamoeba histolytica EHI_117370   hypothetical protein
Entamoeba histolytica EHI_166590   S1 RNA binding domain-containing protein
Entamoeba histolytica EHI_077270   S1 RNA binding domain-containing protein
Entamoeba histolytica EHI_124060   ;Alias
Echinococcus multilocularis EmuJ_000014400   programmed cell death protein 11
Echinococcus multilocularis EmuJ_000288700   rRNA processing protein
Echinococcus multilocularis EmuJ_001068100   protein rrp5
Giardia lamblia GL50803_14702   RRNA biogenesis protein RRP5
Homo sapiens ENSG00000148843   programmed cell death 11
Leishmania braziliensis LbrM.20.4880   rRNA biogenesis protein-like protein
Leishmania donovani LdBPK_200710.1   rRNA biogenesis protein-like protein
Leishmania infantum LinJ.20.0710   rRNA biogenesis protein-like protein
Leishmania major LmjF.20.0650   rRNA biogenesis protein-like protein
Leishmania mexicana LmxM.20.0650   rRNA biogenesis protein-like protein
Loa Loa (eye worm) LOAG_10419   hypothetical protein
Loa Loa (eye worm) LOAG_05077   hypothetical protein
Mycobacterium leprae ML1382   PROBABLE RIBOSOMAL PROTEIN S1 RPSA
Mus musculus ENSMUSG00000025047   programmed cell death 11
Mycobacterium tuberculosis Rv1630   30S ribosomal protein S1 RpsA
Mycobacterium ulcerans MUL_1612   30S ribosomal protein S1
Neospora caninum NCLIV_014030   30S ribosomal protein S1, putative
Neospora caninum NCLIV_047560   hypothetical protein
Oryza sativa 4332652   Os03g0315800
Oryza sativa 4342673   Os07g0203300
Plasmodium berghei PBANKA_1037600   rRNA biogenesis protein RRP5, putative
Plasmodium berghei PBANKA_1425600   RNA-binding protein, putative
Plasmodium falciparum PF3D7_1404500   rRNA biogenesis protein RRP5, putative
Plasmodium falciparum PF3D7_0811900   RNA-binding protein, putative
Plasmodium knowlesi PKNH_1353600   rRNA biogenesis protein RRP5, putative
Plasmodium knowlesi PKNH_1428800   RNA-binding protein, putative
Plasmodium vivax PVX_086210   rRNA biogenesis protein RRP5, putative
Plasmodium vivax PVX_123175   hypothetical protein, conserved
Plasmodium yoelii PY00994   rrp5 protein homolog
Plasmodium yoelii PY00746   S1 RNA binding domain, putative
Saccharomyces cerevisiae YMR229C   Rrp5p
Schistosoma japonicum Sjp_0041520   ko:K09522 DnaJ homolog, subfamily C, member 2, putative
Schistosoma japonicum Sjp_0207360   Protein RRP5 homolog, putative
Schistosoma mansoni Smp_105930   programmed cell death protein
Schistosoma mansoni Smp_105920   hypothetical protein
Schmidtea mediterranea mk4.061543.00  
Schmidtea mediterranea mk4.037673.00  
Schmidtea mediterranea mk4.001099.03   Putative programmed cell death protein 11
Trypanosoma brucei gambiense Tbg972.1.670   rRNA biogenesis protein, putative
Trypanosoma brucei Tb927.1.1370   rRNA biogenesis protein, putative
Trypanosoma congolense TcIL3000_1_820   rRNA biogenesis protein, putative
Trypanosoma congolense TcIL3000_0_17790   rRNA biogenesis protein, putative
Trypanosoma cruzi TcCLB.506479.50   rRNA biogenesis protein, putative
Trypanosoma cruzi TcCLB.503803.10   rRNA biogenesis protein, putative
Toxoplasma gondii TGME49_225125   pre-rRNA processing protein
Toxoplasma gondii TGME49_286620   S1 RNA binding domain-containing protein
Treponema pallidum TP0279   bifunctional cytidylate kinase/ribosomal protein S1
Theileria parva TP01_0237   hypothetical protein
Trichomonas vaginalis TVAG_292010   programmed cell death protein, putative
Wolbachia endosymbiont of Brugia malayi Wbm0059   30S ribosomal protein S1

Essentiality

Rv1630 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1658 this record Mycobacterium tuberculosis essential nmpdr
Tb927.1.1370 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.1.1370 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.1.1370 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.1.1370 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0911 Escherichia coli essential goodall
CELE_C16A3.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C16A3.3 Caenorhabditis elegans larval arrest wormbase
CELE_C16A3.3 Caenorhabditis elegans slow growth wormbase
CELE_C16A3.3 Caenorhabditis elegans sterile wormbase
YMR229C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1037600 Plasmodium berghei Slow plasmo
TGME49_286620 Toxoplasma gondii Probably essential sidik
TGME49_225125 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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 Rv1630 (Mycobacterium tuberculosis), 30S ribosomal protein S1 RpsA
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