Detailed view for Rv3433c

Basic information

TDR Targets ID: 9126
Mycobacterium tuberculosis, Conserved protein
Source Database / ID:  Tuberculist 

pI: 5.9424 | Length (AA): 473 | MW (Da): 46857 | 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

PF01256   Carbohydrate kinase
PF03853   YjeF-related protein N-terminus

Gene Ontology

Mouse over links to read term descriptions.
GO:0052855   GO:ADP-dependent NAD(P)H-hydrate dehydratase 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
5 473 3rss (A) 0 488 27.00 0 1 1.17444 0.42
202 470 2r3b (A) 0 270 23.00 0 1 0.82161 -0.36
209 473 3rpz (A) 6 275 28.00 0 1 0.852154 -0.31
344 456 1ub0 (A) 133 253 37.00 0.4 1 0.634301 -0.14

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 0-20% percentile Dormant phase. 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_127151)

Species Accession Gene Product
Arabidopsis thaliana AT5G19150   pfkB-like carbohydrate kinase family protein
Brugia malayi Bm1_07040   YjeF-related protein, C-terminus containing protein
Candida albicans CaO19.11002   similar to S. cerevisiae YKL151C
Candida albicans CaO19.3508   similar to S. cerevisiae YKL151C
Caenorhabditis elegans CELE_R107.2   Protein R107.2
Cryptosporidium hominis Chro.70406   ENSANGP00000015295
Cryptosporidium parvum cgd7_3640   YjeF family of predicted nucleotide binding proteins
Dictyostelium discoideum DDB_G0290799   uncharacterized protein family, carbohydrate kinase-related
Drosophila melanogaster Dmel_CG10424   CG10424 gene product from transcript CG10424-RA
Escherichia coli b4167   bifunctional NAD(P)H-hydrate repair enzyme
Echinococcus granulosus EgrG_000434000   carbohydrate kinase domain containing protein
Entamoeba histolytica EHI_194450   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000434000   carbohydrate kinase domain containing protein
Giardia lamblia GL50803_4255   Sugar kinase, putative
Homo sapiens ENSG00000213995   carbohydrate kinase domain containing
Leishmania braziliensis LbrM.14.1360   hypothetical protein, conserved
Leishmania donovani LdBPK_141270.1   Bifunctional NAD(P)H-hydrate repair enzyme
Leishmania infantum LinJ.14.1270   hypothetical protein, conserved
Leishmania major LmjF.14.1190   hypothetical protein, conserved
Leishmania mexicana LmxM.14.1190   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04267   hypothetical protein
Mycobacterium leprae ML0373   Conserved hypothetical protein
Mus musculus ENSMUSG00000031505   carbohydrate kinase domain containing
Mycobacterium tuberculosis Rv3433c   Conserved protein
Mycobacterium ulcerans MUL_0877   transmembrane protein
Oryza sativa 4350275   Os11g0276300
Plasmodium berghei PBANKA_0905100   ATP-dependent (S)-NAD(P)H-hydrate dehydratase, putative
Plasmodium falciparum PF3D7_1143900   ATP-dependent (S)-NAD(P)H-hydrate dehydratase, putative
Plasmodium knowlesi PKNH_0941800   ATP-dependent (S)-NAD(P)H-hydrate dehydratase, putative
Plasmodium vivax PVX_092800   carbohydrate kinase, putative
Plasmodium yoelii PY02608   YjeF-related protein, C-terminus
Saccharomyces cerevisiae YKL151C   NADHX dehydratase
Schistosoma japonicum Sjp_0303960   similar to Uncharacterized protein FLJ10769 homolog precursor, putative
Schistosoma mansoni Smp_000470   hypothetical protein
Schmidtea mediterranea mk4.003659.00   ATP-dependent
Trypanosoma brucei gambiense Tbg972.7.4200   hypothetical protein, conserved
Trypanosoma brucei Tb927.7.3770   Bifunctional NAD(P)H-hydrate repair enzyme
Trypanosoma congolense TcIL3000_7_3030   Bifunctional NAD(P)H-hydrate repair enzyme
Trypanosoma cruzi TcCLB.506795.44   Bifunctional NAD(P)H-hydrate repair enzyme
Trypanosoma cruzi TcCLB.509937.20   Bifunctional NAD(P)H-hydrate repair enzyme
Toxoplasma gondii TGME49_258160   carbohydrate kinase
Trichomonas vaginalis TVAG_468220   conserved hypothetical protein
Trichomonas vaginalis TVAG_051000   conserved hypothetical protein

Essentiality

Rv3433c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3494 this record Mycobacterium tuberculosis non-essential nmpdr
Tb927.7.3770 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.3770 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.3770 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.3770 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4167 Escherichia coli non-essential goodall
PBANKA_0905100 Plasmodium berghei Dispensable plasmo
TGME49_258160 Toxoplasma gondii Probably non-essential sidik
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
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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
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 Rv3433c (Mycobacterium tuberculosis), Conserved protein
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