Detailed view for Rv2788

Basic information

TDR Targets ID: 981107
Mycobacterium tuberculosis, Probable transcriptional repressor SirR
Source Database / ID:  Tuberculist 

pI: 4.8698 | Length (AA): 228 | MW (Da): 24919 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF01325  
PF02742  
PF04023  

Gene Ontology

Mouse over links to read term descriptions.
GO:0006355   regulation of transcription, DNA-dependent  
GO:0003677   DNA binding  
GO:0046983   protein dimerization activity  
GO:0046914   transition metal ion binding  
GO:0043565   sequence-specific DNA binding  
GO:0003700   transcription factor activity  

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
7 227 1fx7 (A) 1 228 26.00 0.0000000000067 1 1.3186 -0.66
10 79 2obp (A) 13 87 21.00 0 1 0.703818 -1.8
10 140 2x4h (A) 10 137 27.00 0 1 1.04336 -1.44
12 227 5cvi (A) 3 213 35.00 0 1 1.44067 -0.7

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_132027)

Species Accession Gene Product
Escherichia coli b0817   Mn(2+)-responsive manganese regulon transcriptional regulator
Mycobacterium leprae ML1013c   IRON-DEPENDENT REPRESSOR AND ACTIVATOR IDER
Mycobacterium tuberculosis Rv2711   Iron-dependent repressor and activator IdeR
Mycobacterium tuberculosis Rv2788   Probable transcriptional repressor SirR
Mycobacterium ulcerans MUL_2145   transcriptional repressor SirR
Mycobacterium ulcerans MUL_3351   iron-dependent repressor and activator IdeR
Treponema pallidum TP0167   cation-activated repressor protein (troR)

Essentiality

Rv2788 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0817 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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
Species Known druggable target Linked compounds Reference
Mycobacterium tuberculosis Iron-dependent repressor and activator IdeR Compounds References
Mycobacterium leprae IRON-DEPENDENT REPRESSOR AND ACTIVATOR IDER Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.1974 0.6724 0.6724
0.2191 0.6783 0.6782
0.1821 0.6796 0.6793
0.2245 0.5181 0.6661
0.1878 0.6792 0.6791
0.1958 0.6794 0.6792
0.1841 0.6792 0.6791
0.1805 0.6791 0.6791
0.1841 0.6792 0.6791
0.1821 0.6796 0.6793
0.2245 0.6798 0.6797
0.1841 0.6792 0.6791
0.1821 0.6796 0.6793
0.1877 0.6724 0.6724
0.1805 0.679 0.679
0.1893 0.6763 0.6724
0.1918 0.6791 0.6791
0.2245 0.5181 0.6661
0.1841 0.6791 0.6791
0.1821 0.6796 0.6793
0.2245 0.5181 0.6661
0.1877 0.6724 0.6724

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 Rv2788 (Mycobacterium tuberculosis), Probable transcriptional repressor SirR
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