Detailed view for Rv2488c

Basic information

TDR Targets ID: 8566
Mycobacterium tuberculosis, Probable transcriptional regulatory protein (LuxR-family)
Source Database / ID:  Tuberculist 

pI: 6.4016 | Length (AA): 1137 | MW (Da): 120818 | Paralog Number: 3

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

PF00196   Bacterial regulatory proteins, luxR family

Gene Ontology

Mouse over links to read term descriptions.
GO:0035556   GO:intracellular signal transduction  

GO:0006355   regulation of transcription, DNA-dependent  
GO:0005622   intracellular  
GO:0043565   sequence-specific DNA binding  
GO:0016849   phosphorus-oxygen lyase activity  
GO:0005515   protein binding  
GO:0003700   transcription factor activity  
GO:0003677   DNA binding  
GO:0000156   two-component response regulator activity  
GO:0009190   cyclic nucleotide biosynthetic process  
GO:0007242   intracellular signaling cascade  
GO:0006952   defense response  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 10 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
4 178 6fht (A) 490 690 24.00 0.0000018 0.98 0.321814 -0.33
23 190 1y10 (A) 179 354 19.00 0.00087 0.68 0.322657 -0.4
52 180 1ybt (A) 291 424 27.00 0.000000000013 1 0.542356 -1.62
53 181 1wc3 (A) 1007 1169 24.00 0.000000091 1 0.263356 -1.03
238 577 2a5y (C) 126 543 14.00 0 1 0.363433 0.43
818 926 1c1d (A) 190 293 38.00 0.95 0.15 0.311866 1.3
1042 1128 5hev (A) 107 207 38.00 0.00079 1 0.421517 -0.34
1056 1128 3p7n (A) 149 221 38.00 0.00056 1 0.716204 -1.81
1070 1135 1x3u (A) 142 204 41.00 0.3 1 0.598047 -0.79
1070 1128 1je8 (A) 156 214 37.00 0 1 0.632291 -1.47

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 Dormant phase, Dormant phase. hasan 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_160474)

Species Accession Gene Product
Mycobacterium leprae ML1753c   PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
Mycobacterium tuberculosis Rv0890c   Probable transcriptional regulatory protein (probably LuxR-family)
Mycobacterium tuberculosis Rv2488c   Probable transcriptional regulatory protein (LuxR-family)
Mycobacterium tuberculosis Rv0386   Probable transcriptional regulatory protein (probably LuxR/UhpA-family)
Mycobacterium tuberculosis Rv1358   Probable transcriptional regulatory protein
Mycobacterium ulcerans MUL_4753   serine/threonine-protein kinase transcriptional regulatory protein PknK_3
Mycobacterium ulcerans MUL_2743   LuxR family transcriptional regulator
Mycobacterium ulcerans MUL_2555   hypothetical protein

Essentiality

Rv2488c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu389 Mycobacterium tuberculosis non-essential nmpdr
mtu2531 this record Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0523 0.2639 0.3942
0.0268 1 0.5
0.0357 0.789 0.7547
0.0159 0.4018 1
0.0198 0.5 0.5
0.0478 0.2931 0
0.0781 0.5 0.5
0.0531 0.6046 1
0.0487 0.2979 0.5
0.0636 0.7588 1
0.0128 0.6741 0.8422
0.0176 0.5 0.5
0.086 1 0.5
0.0347 0.9499 0.9748
0.0141 0.8074 1
0.086 1 0.5
0.0665 0.965 1
0.0601 0.3411 0.4028
0.0655 0.8632 0.8624
0.1746 0.3248 0.3248
0.0905 0.464 1
0.0293 0.9601 0
0.1143 1 1
0.0176 0.5 0.5
0.0207 0.6534 0.5
0.1143 1 1
0.0238 0.3606 0.8766
0.0347 0.9499 0.9748
0.0552 0.9847 0
0.0467 0.55 0.9843
0.0216 0.7158 0
0.0535 0.9839 0
0.0866 0.9917 0.9917
0.0456 0.5035 0.983
0.0456 0.5035 0.983
0.024 0.3813 0.5
0.0689 0.4158 0.7704
0.0441 0.5505 1
0.0261 0.9267 0.9267
0.0601 0.3411 0.4028
0.0965 0.993 0.993
0.0257 0.2722 0.5
0.0711 0.2634 0.3937
0.0422 0.2853 0.98
0.1332 0.9955 0
0.0066 1 0.5
0.0531 0.2552 0.2546
0.0357 0.789 0.7547
0.0227 0.3094 1
0.016 0.3757 1
0.0157 1 1
0.0176 0.5 0.5
0.0712 0.8911 1
0.024 0.279 1
0.0201 1 1
0.0176 0.5 0.5
0.1298 0.5 0.5
0.0753 0.5 0.5
0.0238 0.3606 0.8766
0.1143 1 1
0.0535 0.9839 0
0.0064 0.5 0.5
0.0531 0.6046 1
0.0079 0.8651 0.5
0.0486 0.4614 0.9376
0.0522 0.9877 0
0.0535 0.9839 0
0.0523 0.2639 0.3942
0.2414 0.9979 0.9979
0.0399 0.6993 1
0.0606 1 1
0.0554 0.985 0
0.0535 0.9839 0
0.0665 1 0.5
0.1454 0.9119 0.9961
0.0535 0.9839 0
0.0238 0.3883 0.5
0.0132 0.8998 0.8879
0.1865 0.5077 0.5074
0.0668 0.8261 1
0.0655 0.8632 0.8624
0.0395 0.7562 0.7371
0.095 0.5 0.5
0.1129 0.9943 0.9943
0.0066 0.2863 0.5
0.0547 0.9852 0.9852
0.0477 0.9831 0
0.0851 0.2525 0.7782
0.0346 1 0.5
0.0399 0.6993 1
0.0665 0.965 1
0.0238 0.3606 0.8766
0.0176 0.5 0.5
0.1203 0.5 0.5
0.0679 1 1
0.0203 0.2885 0.5
0.0317 0.3548 0.5
0.0141 0.8074 1
0.0333 1 0.5
0.0176 0.5 0.5
0.0153 0.5107 0.6267
0.0636 0.7588 1
0.1135 0.4752 1
0.0665 0.9873 0.9873
0.015 0.3877 0.5
0.0333 0.6438 0.6223
0.0367 0.4774 0.9758
0.0389 0.7254 1
0.0624 0.2768 0.5
0.0066 0.2863 0.5
0.0628 0.8547 1
0.0401 0.2782 1
0.0333 0.6438 0.6223
0.0133 0.3358 0
0.0149 0.5 0.5
0.0367 0.9701 0
0.138 1 1
0.0599 0.5862 0
0.0624 1 1
0.0256 0.2558 0.9599
0.0063 0.3345 0.4343
0.0668 0.8261 1
0.0256 0.2558 0.9599
0.0584 0.9836 0.9836
0.1109 1 0.5
0.0767 0.5 0.5
0.0272 0.5639 1
0.0245 0.6283 0.5

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 Rv2488c (Mycobacterium tuberculosis), Probable transcriptional regulatory protein (LuxR-family)
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