TDR Targets

Detailed view for Rv1837c

Basic information

TDR Targets ID: 6139
Mycobacterium tuberculosis, Malate synthase G GlcB
Source Database / ID: Tuberculist

pI: 4.8271 | Length (AA): 741 | MW (Da): 80403 | 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

Network

Pfam domains

PF01274 Malate synthase

Gene Ontology

Mouse over links to read term descriptions.

GO:0004474 malate synthase activity
GO:0003824 catalytic activity
GO:0006097 glyoxylate cycle

Metabolic Pathways

Pyruvate metabolism (KEGG)
Glyoxylate and dicarboxylate metabolism (KEGG)
Global map (KEGG)
Biosynthesis of secondary metabolites (KEGG)
Microbial metabolism in diverse environments (KEGG)
Carbon metabolism (KEGG)

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg	Target End	Template	Template Beg	Template End	Identity	Evalue	Model Score	MPQS	zDope
2	727	3s9z (A)	2	727	99.99	0	1	2.20786	-1.46

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:

1N8I:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

1N8W:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

2GQ3:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

3S9I:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

3S9Z:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

3SAD:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

3SAZ:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

3SB0:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5C7V:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5C9R:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5C9U:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5C9W:

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5C9X:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CAH:

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5CAK:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CBB:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CBI:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CBJ:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CC3:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CC5:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CC6:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CC7:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CCZ:

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5CEW:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CJM:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5CJN:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5DRC:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5DRI:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5DX7:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5E9X:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5ECV:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5H8M:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5H8P:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5H8U:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

5T8G:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6APZ:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6AS6:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6ASU:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6AU9:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6AXB:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6BA7:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6BU1:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6C2X:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6C6O:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6C7B:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6C8P:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6DKO:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6DL9:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6DLJ:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

6DNP:

Resolution	Method	# Atoms	# Residues	Dep. Date	Pub. Date	Mod. Date

Expression

Upregulation Percent	Ranking	Stage	Dataset
Lower 0-20% 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_159543)

Species	Accession	Gene Product
Escherichia coli	b2976	malate synthase G
Mycobacterium leprae	ML2069	PROBABLE MALATE SYNTHASE G GLCB
Mycobacterium tuberculosis	Rv1837c	Malate synthase G GlcB
Mycobacterium ulcerans	MUL_3055	malate synthase G

Essentiality

Rv1837c has direct evidence of essentiality

Gene/Ortholog	Organism	Phenotype	Source Study
mtu1867 this record	Mycobacterium tuberculosis	non-essential	nmpdr
b2976	Escherichia coli	non-essential	goodall

Show/Hide essentiality data references

shigen

Profiling of E. coli Chromosome (PEC)

National Institute of Genetics, Japan

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

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.

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.

alsford

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

Genome Res 2011, 21:915-924

wormbase

C. elegans RNAi experiments

WormBase web site, http://www.wormbase.org, release WS170

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

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)

Annotated phenotypes:

Affected Entity	Phenotypic quality	Occurs in	Occurs at	Evidence	Observed in	Drugs/Inhibitors
catalytic activity (GO:0003824)	decreased (PATO:0000468)	in vitro (MI:0492)		inferred from specific protein inhibition (ECO:0000020)	Mycobacterium tuberculosis	311792 320674 574153 579838
Annotator:	crowther@u.washington.edu.	Comment:	2008-01-02.		References:	12393860
adhesion to host (GO:0044406)	decreased (PATO:0000468)			inferred from specific protein inhibition (ECO:0000020)	Mycobacterium tuberculosis	No drug identifiers listed for this gene.
Annotator:	crowther@u.washington.edu.	Comment:	2008-01-02.		References:	16677310

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

Compound	Source	Reference
	Curated by TDRTargets	References
	Curated by TDRTargets	References
	Curated by TDRTargets	References
	Curated by TDRTargets	References

Predicted associations

By orthology with druggable targets

Species	Known druggable target	Linked compounds	Reference
Mycobacterium leprae	PROBABLE MALATE SYNTHASE G GLCB	Compounds	References

By sequence similarity to non orthologous druggable targets

No additional associated druggable targets

Ranking Plot

Putative Drugs List

Raw	Global	Species
0.2253	1	1
0.2556	1	1
0.2779	0.2998	0.3225
0.056	1	1
0.2078	0.3617	0.3771
0.2253	1	1
0.2253	1	1
0.2572	0.3776	0.6588
0.373	0.3242	0.352
0.2292	0.4677	1
0.2523	1	1
0.2572	0.3776	0.6588
0.2572	0.3776	0.6588
0.2295	1	1
0.2253	1	1
0.277	1	0.5
0.2253	1	1
0.2253	1	1
0.1599	0.3225	0.4484
0.2203	1	0.5
0.2572	0.3776	0.6588
0.2028	0.2775	0.5208
0.1994	1	0.5
0.2323	0.5	0.5
0.2253	1	1
0.2323	0.5	0.5
0.2028	0.2775	0.5208
0.2259	0.3137	0.5209
0.2375	0.3616	0.3768
0.2572	0.3776	0.6588
0.2323	1	0.5
0.2478	1	1
0.31	0.3242	0.3335
0.2253	1	1
0.2259	1	1
0.2754	1	1
0.1616	0.2529	0.3685
0.236	1	1
0.277	1	0.5
0.2754	0.2954	1
0.2342	0.3621	0.3774
0.1038	0.3378	0.3592
0.2323	1	0.5
0.1038	0.3378	0.3592
0.2253	1	1
0.2342	0.3621	0.3774
0.2572	0.3776	0.6588
0.2203	1	1
0.2253	1	1
0.2478	1	1
0.2253	1	1
0.2203	1	0.5
0.1847	0.3587	0.3769
0.2572	0.3776	0.6588
0.2253	1	1
0.2478	1	1
0.2478	1	1

Assayability

Assay information

Assay for Malate Synthase (4.1.3.2 ) Sigma-Aldrich
Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

2 literature references were collected for this gene.

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	Rv1837c (Mycobacterium tuberculosis), Malate synthase G GlcB

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