Detailed view for Rv3700c

Basic information

TDR Targets ID: 9721
Mycobacterium tuberculosis, Conserved hypothetical protein
Source Database / ID:  Tuberculist 

pI: 4.9707 | Length (AA): 390 | MW (Da): 40446 | 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

PF00266   Aminotransferase class-V

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Metabolic Pathways

Histidine metabolism (KEGG)

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
9 390 2dkj (A) 9 392 18.00 0 1 1.06249 0.7
13 387 1t3i (A) 8 414 22.00 0 1 1.16354 0.18
15 386 1jf9 (A) 5 405 22.00 0 1 1.14285 0.21
29 229 3vax (A) 3 213 34.00 0.0000028 1 0.712585 0.96
67 248 4j8l (A) 50 229 18.00 0.19 1 0.704667 -0.38

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
Lower 20-40% 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_127282)

Species Accession Gene Product
Arabidopsis thaliana AT2G13360   alanine--glyoxylate aminotransferase
Candida albicans CaO19.8679   similar to C terminus of S. cerevisiae AGX1 (YFL030W) putative alanine glyoxylate aminotransferase
Candida albicans CaO19.1079   similar to N terminus of S. cerevisiae AGX1 (YFL030W) putative alanine glyoxylate aminotransferase
Candida albicans CaO19.8680   similar to N terminus of S. cerevisiae AGX1 (YFL030W) putative alanine glyoxylate aminotransferase
Candida albicans CaO19.1078   similar to C terminus of S. cerevisiae AGX1 (YFL030W) putative alanine glyoxylate aminotransferase
Caenorhabditis elegans CELE_T14D7.1   Protein T14D7.1
Dictyostelium discoideum DDB_G0289923   alanine-glyoxylate aminotransferase
Drosophila melanogaster Dmel_CG3926   Serine pyruvate aminotransferase
Giardia lamblia GL50803_3313   Serine-pyruvate aminotransferase
Homo sapiens ENSG00000172482   alanine-glyoxylate aminotransferase
Leishmania braziliensis LbrM.03.0060   2-aminoethylphosphonate:pyruvateaminotransferas e-like protein
Leishmania donovani LdBPK_030040.1   2-aminoethylphosphonate:pyruvateaminotransferas e-like protein
Leishmania infantum LinJ.03.0040   2-aminoethylphosphonate:pyruvateaminotransferas e-like protein
Leishmania major LmjF.03.0040   2-aminoethylphosphonate:pyruvateaminotransferas e-like protein
Leishmania mexicana LmxM.03.0040   2-aminoethylphosphonate:pyruvateaminotransferas e-like protein
Mus musculus ENSMUSG00000026272   alanine-glyoxylate aminotransferase
Mycobacterium tuberculosis Rv3700c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_4284   selenocysteine lyase, CsdB
Neospora caninum NCLIV_016150   Serine--pyruvate transaminase (EC 2.6.1.51), related
Oryza sativa 4345962   Os08g0502700
Saccharomyces cerevisiae YFL030W   alanine--glyoxylate transaminase
Schmidtea mediterranea mk4.050532.00  
Trypanosoma cruzi TcCLB.509693.100   2-aminoethylphosphonate:pyruvateaminotransferase- likeprotein,putative
Trypanosoma cruzi TcCLB.506457.60   2-aminoethylphosphonate:pyruvateaminotransferase- likeprotein,putative
Toxoplasma gondii TGME49_239530   alanine-glyoxylate aminotransferase

Essentiality

Rv3700c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3763 this record Mycobacterium tuberculosis non-essential nmpdr
TGME49_239530 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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.

User comments

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Gene identifier Rv3700c (Mycobacterium tuberculosis), Conserved hypothetical protein
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