Detailed view for Rv1409

Basic information

TDR Targets ID: 7008
Mycobacterium tuberculosis, Probable bifunctional riboflavin biosynthesis protein RibG : diaminohydroxyphosphoribosylaminopyrimidine deaminase (riboflavin-s
Source Database / ID:  Tuberculist 

pI: 6.8451 | Length (AA): 339 | MW (Da): 35367 | Paralog Number: 0

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

PF00383   Cytidine and deoxycytidylate deaminase zinc-binding region
PF01872   RibD C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008703   5-amino-6-(5-phosphoribosylamino)uracil reductase activity  
GO:0050661   NADP binding  
GO:0016787   hydrolase activity  
GO:0008835   diaminohydroxyphosphoribosylaminopyrimidine deaminase activity  
GO:0008270   zinc ion binding  
GO:0003824   catalytic activity  
GO:0009231   riboflavin biosynthetic process  
GO:0055114   oxidation reduction  

Structural information

Modbase 3D models:

There are 5 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
1 148 3dh1 (A) 14 173 24.00 0 0.99 0.575978 -0.5
4 338 3zpg (A) 2 356 28.00 0 1 1.2484 0.46
11 151 1p6o (A) 13 150 19.00 0 1 0.598329 -0.72
13 337 3zpg (A) 11 355 41.00 0 1 1.3687 0.14
13 337 2g6v (A) 7 365 42.00 0 1 1.2357 0.47

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
Mid 40-60% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_127122)

Species Accession Gene Product
Arabidopsis thaliana AT3G47390   putative pyrimidine reductase
Arabidopsis thaliana AT4G20960   diaminohydroxyphosphoribosylaminopyrimidine deaminase
Brugia malayi Bm1_52340   hypothetical protein
Brugia malayi Bm1_38625   hypothetical protein
Candida albicans CaO19.13697   biosynthesis of riboflavin
Candida albicans CaO19.6341   biosynthesis of riboflavin
Caenorhabditis elegans CELE_C07G3.2   Protein IRG-1
Caenorhabditis elegans CELE_T24A6.7   Protein T24A6.7
Chlamydia trachomatis CT_730   bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductase
Dictyostelium discoideum DDB_G0281625   hypothetical protein
Dictyostelium discoideum DDB_G0283925   hypothetical protein
Escherichia coli b0414   fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase
Escherichia coli b0798   DUF1768 family protein
Entamoeba histolytica EHI_017590   hypothetical protein, conserved
Leishmania braziliensis LbrM.06.0110   hypothetical protein, conserved
Leishmania donovani LdBPK_060130.1   hypothetical protein, conserved
Leishmania infantum LinJ.06.0130   hypothetical protein, conserved
Leishmania major LmjF.06.0130   hypothetical protein, conserved
Leishmania mexicana LmxM.06.0130   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_01183   hypothetical protein
Loa Loa (eye worm) LOAG_02092   hypothetical protein
Loa Loa (eye worm) LOAG_07594   hypothetical protein
Mycobacterium leprae ML0555   Probable bifunctional riboflavin-specific deaminase/reductase RibG: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Ribof
Mycobacterium tuberculosis Rv1409   Probable bifunctional riboflavin biosynthesis protein RibG : diaminohydroxyphosphoribosylaminopyrimidine deaminase (riboflavin-s
Mycobacterium ulcerans MUL_1805   bifunctional riboflavin biosynthesis protein RibG
Oryza sativa 4329349   Os02g0473000
Oryza sativa 4331409   Os03g0117200
Onchocerca volvulus OVOC6592  
Onchocerca volvulus OVOC4753  
Onchocerca volvulus OVOC12609  
Saccharomyces cerevisiae YBR153W   Rib7p
Schmidtea mediterranea mk4.058156.01  
Schmidtea mediterranea mk4.000002.47  
Schmidtea mediterranea mk4.058156.02  
Schmidtea mediterranea mk4.000734.03  
Trypanosoma brucei gambiense Tbg972.7.5460   hypothetical protein, conserved
Trypanosoma brucei Tb927.7.4780   conserved hypothetical protein, putative
Trypanosoma congolense TcIL3000_7_3950   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.508577.150   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.507521.60   hypothetical protein, conserved
Trichomonas vaginalis TVAG_227690   conserved hypothetical protein
Wolbachia endosymbiont of Brugia malayi Wbm0026   pyrimidine deaminase and reductase

Essentiality

Rv1409 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1432 this record Mycobacterium tuberculosis essential nmpdr
Tb927.7.4780 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.4780 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.7.4780 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.7.4780 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0414 Escherichia coli essential goodall
b0798 Escherichia coli non-essential goodall
YBR153W Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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.

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Gene identifier Rv1409 (Mycobacterium tuberculosis), Probable bifunctional riboflavin biosynthesis protein RibG : diaminohydroxyphosphoribosylaminopyrimidine deaminase (riboflavin-s
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