Detailed view for Rv3107c

Basic information

TDR Targets ID: 5645
Mycobacterium tuberculosis, Possible alkyldihydroxyacetonephosphate synthase AgpS (alkyl-DHAP synthase) (alkylglycerone-phosphate synthase)
Source Database / ID:  Tuberculist 

pI: 6.5016 | Length (AA): 527 | MW (Da): 56521 | 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

PF01565   FAD binding domain
PF02913   FAD linked oxidases, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016614   oxidoreductase activity, acting on CH-OH group of donors  
GO:0016491   oxidoreductase activity  
GO:0003824   catalytic activity  
GO:0050660   FAD binding  
GO:0055114   oxidation reduction  

Metabolic Pathways

Ether lipid metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 3 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
1 525 4bby (A) 90 658 26.00 0 1 1.2658 0.13
1 519 5ae2 (A) 90 652 27.00 0 1 1.27112 0.2
25 151 5khn (B) 577 697 35.00 0.88 0.26 0.247787 1.71

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. murphy
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_130256)

Species Accession Gene Product
Brugia malayi Bm1_07035   alkyldihydroxyacetonephosphate synthase
Caenorhabditis elegans CELE_Y50D7A.7   Protein ADS-1
Dictyostelium discoideum DDB_G0286183   alkyl-dihydroxyacetonephosphate synthase
Drosophila melanogaster Dmel_CG10253   CG10253 gene product from transcript CG10253-RB
Escherichia coli b4463   putative FAD-containing dehydrogenase
Homo sapiens ENSG00000018510   alkylglycerone phosphate synthase
Leishmania braziliensis LbrM.30.0130   alkyldihydroxyacetonephosphate synthase
Leishmania donovani LdBPK_300120.1   alkyldihydroxyacetonephosphate synthase
Leishmania infantum LinJ.30.0120   alkyldihydroxyacetonephosphate synthase
Leishmania major LmjF.30.0120   alkyldihydroxyacetonephosphate synthase
Leishmania mexicana LmxM.29.0120   alkyl dihydroxyacetonephosphate synthase
Loa Loa (eye worm) LOAG_04268   alkyldihydroxyacetonephosphate synthase
Mus musculus ENSMUSG00000042410   alkylglycerone phosphate synthase
Mycobacterium tuberculosis Rv3107c   Possible alkyldihydroxyacetonephosphate synthase AgpS (alkyl-DHAP synthase) (alkylglycerone-phosphate synthase)
Mycobacterium tuberculosis Rv2251   Possible flavoprotein
Mycobacterium ulcerans MUL_1298   flavoprotein
Schmidtea mediterranea mk4.000265.05   Alkyldihydroxyacetonephosphate synthase
Trypanosoma brucei gambiense Tbg972.6.1150   alkyl-dihydroxyacetone phosphate synthase,alkyl-DHAP synthase,alkylglycerone-phosphate synthase
Trypanosoma brucei Tb927.6.1500   alkyl-dihydroxyacetone phosphate synthase
Trypanosoma congolense TcIL3000_0_37370   alkyl-dihydroxyacetone phosphate synthase
Trypanosoma congolense TcIL3000_6_980   alkylglycerone-phosphate synthase, putative
Trypanosoma cruzi TcCLB.505807.110   alkyl-dihydroxyacetone phosphate synthase, putative
Trypanosoma cruzi TcCLB.503815.10   alkyl-dihydroxyacetone phosphate synthase, putative

Essentiality

Rv3107c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
this record Mycobacterium tuberculosis non-essential nmpdr
mtu2286 Mycobacterium tuberculosis essential nmpdr
Tb927.6.1500 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.1500 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.1500 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.6.1500 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4463 Escherichia coli non-essential goodall
CELE_Y50D7A.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y50D7A.7 Caenorhabditis elegans larval arrest wormbase
CELE_Y50D7A.7 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.

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

Druggability index (range: 0 to 1): 0.3

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 Rv3107c (Mycobacterium tuberculosis), Possible alkyldihydroxyacetonephosphate synthase AgpS (alkyl-DHAP synthase) (alkylglycerone-phosphate synthase)
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