Detailed view for Rv3793

Basic information

TDR Targets ID: 5926
Mycobacterium tuberculosis, Integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase)
Source Database / ID:  Tuberculist 

pI: 10.1407 | Length (AA): 1094 | MW (Da): 117490 | Paralog Number: 2

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 13

Druggability Group : DG3

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

PF04602   Mycobacterial cell wall arabinan synthesis protein
PF14896   EmbC C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0071766   GO:Actinobacterium-type cell wall biogenesis  

GO:0052636   GO:arabinosyltransferase activity  

GO:0016021   integral to membrane  
GO:0009252   peptidoglycan biosynthetic process  

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
56 221 3byw (A) 39 195 25.00 0 0.75 0.377437 -0.36
57 212 3byw (A) 40 181 31.00 0.0000029 0.97 0.366296 0.42
269 679 5ezm (A) 27 432 21.00 0 0.73 0.337586 1.3
735 1067 3pty (A) 735 1067 99.99 0 1 1.23709 -0.24

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:

PDB tag
  • 3PTY:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. 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_166834)

Species Accession Gene Product
Mycobacterium leprae ML0106c   Probable integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase)
Mycobacterium leprae ML0104c   Probable integral membrane indolylacetylinositol arabinosyltransferase EmbB (arabinosylindolylacetylinositol synthase)
Mycobacterium leprae ML0105c   Probable integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase)
Mycobacterium tuberculosis Rv3795   Integral membrane indolylacetylinositol arabinosyltransferase EmbB (arabinosylindolylacetylinositol synthase)
Mycobacterium tuberculosis Rv3793   Integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase)
Mycobacterium tuberculosis Rv3794   Integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase)
Mycobacterium ulcerans MUL_4974   integral membrane indolylacetylinositol arabinosyltransferase EmbB
Mycobacterium ulcerans MUL_4973   integral membrane indolylacetylinositol arabinosyltransferase EmbA
Mycobacterium ulcerans MUL_4972   integral membrane indolylacetylinositol arabinosyltransferase EmbC

Essentiality

Rv3793 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3862 Mycobacterium tuberculosis essential nmpdr
mtu3860 this record Mycobacterium tuberculosis essential nmpdr
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
response to drug (GO:0042493) increased sensitivity toward (PATO:0001549) inferred from loss-of-function mutant phenotype (ECO:0000016) Mycobacterium smegmatis 526497   540786   540787   540788   546183   557970  
Annotator: crowther@u.washington.edu. Comment: 2007-12-11. References: 11677227

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): 0.5

Known modulators for this target

Compound Source Reference
Curated by TDRTargets References
Curated by TDRTargets References
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 integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase) Compounds References
Mycobacterium tuberculosis Integral membrane indolylacetylinositol arabinosyltransferase EmbB (arabinosylindolylacetylinositol synthase) Compounds References
Mycobacterium leprae Probable integral membrane indolylacetylinositol arabinosyltransferase EmbB (arabinosylindolylacetylinositol synthase) Compounds References
Mycobacterium leprae Probable integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
1.0782 0.8751 1
0.4776 0.8196 1
0.2416 1 1
1.4273 1 1
1.5681 1 1
0.448306 0.440879 0.440729
0.7455 1 1
1.5477 1 1
0.2052 0.3349 0.3767
1.3747 1 1
1.5149 1 1
0.3086 1 0.5
0.5556 0.3989 1
0.1215 0.9721 0.9721
1.3973 1 1
0.101632 0.509307 0.736895
0.3333 0.2722 1
0.1542 1 1
0.5556 0.3989 1
1.0721 1 1
0.425 1 1
1.4267 1 1
1.4897 0.4987 0.4982
0.3205 1 1
1.3973 1 1
0.5206 1 1
0.4776 0.8196 1
0.4557 1 1
0.4097 1 1
0.4198 1 1
0.348 0.2547 0.8186
0.3333 0.2722 1
0.4751 0.2729 1
1.0721 1 1
0.1682 0.4499 1
0.45 1 1
0.1809 0.8514 0.9721
0.2214 0.2816 0.3749
0.2241 0.3692 0.369
0.5206 1 1
0.1971 0.7483 1
0.3112 1 1
0.4776 0.8196 1
1.4718 0.4052 1
0.3333 0.2722 1
0.5556 1 1
0.3205 1 0.5
0.9835 1 1
0.348 0.2535 0.815
0.2053 0.3341 0.9721
0.4776 0.8196 1
1.0006 1 1
0.5556 0.3989 1
0.5556 1 1
1.0607 1 1
1.4267 1 1
1.3948 1 1
1.4267 1 1
0.2984 0.3382 1
0.4776 0.8196 1
0.4776 0.8196 1
0.4751 0.2729 1
0.458 1 1
1.5727 1 1
0.4776 0.8196 1
0.3851 1 1
0.2778 0.332 1
0.5363 1 1
0.4676 0.6677 1
0.4776 0.8196 1
1.4647 1 1
0.3205 1 1
1.4718 0.4052 1
1.0681 1 1
0.1148 0.5059 0.7309
1.47131 1 1
0.4796 0.6642 1
0.3333 0.2722 1
0.3333 0.2722 1
0.1553 0.3021 0.7426
0.3333 0.2722 1
0.996 1 1
0.4198 1 1
0.4776 0.8196 1
0.2778 0.332 1
0.2363 1 1
1.0721 1 1
0.348 0.2547 0.8186
1.4897 0.4987 0.4982
0.5556 0.3989 1
0.458 1 1
0.4751 0.2729 1
1.0721 1 1
1.49 1 1
1.0787 1 1
0.9835 1 1
0.4676 0.6677 1
0.1148 0.7667 1
1.5727 1 1
0.4776 0.8196 1
0.5434 1 1
0.18051 0.785363 0.784379
0.2241 0.6979 0.8811
0.2051 0.694 0.694
1.443 1 1
1.5727 1 1
0.3333 0.2722 1
1.3973 1 1
1.4267 1 1
0.156 0.2792 0.2999
0.4676 0.6677 1
0.3444 0.8852 0.8845
0.4776 0.8196 1
0.7455 1 1
0.2579 0.4675 1
0.5556 1 1
0.9723 1 1
1.5727 1 1
0.6911 1 1
0.4198 1 1
0.239 0.4539 1
0.5556 0.3989 1
0.4776 0.8196 1
1.0888 1 1
0.5556 1 1
0.4776 0.8196 1
0.4676 0.6677 1
0.4751 0.2729 1
0.1919 0.6561 0.891
0.4776 0.8196 1
1.5149 1 1
0.2404 0.6775 1
0.4651 1 1
0.524 1 1
0.22 1 1
0.5556 0.6567 1
0.4776 0.8196 1
1.3948 1 1
1.4897 0.4987 0.4982
1.0006 1 1
0.348 0.2535 0.815
0.458 1 1
1.0787 1 1
0.2052 0.5367 1
0.5223 1 1
0.4776 0.8196 1
0.4751 0.2729 1
0.1919 0.6561 0.891
1.6159 1 1
0.427 0.3518 1
1.4267 1 1
0.1376 0.2626 1
1.4064 1 1
0.101632 0.509307 0.736895
0.2322 0.6259 1
1.0782 0.8751 1
0.4776 0.8196 1
0.4776 0.8196 1
0.4776 0.8196 1
0.4776 0.8196 1
0.0358 1 1
0.2579 0.4675 1
0.2579 1 1
0.4776 0.8196 1
1.531 1 1
0.17961 1 1
1.4897 0.4987 0.4982
1.6159 1 1
0.1682 0.4499 1
0.2667 1 0.5
0.2025 0.8514 0.9721
0.4751 0.2729 1
0.4557 1 1
0.1364 0.302 0.7426
0.3228 0.9722 0.9722
1.0175 1 1
0.4776 0.8196 1
0.2052 0.3349 0.3767
0.9752 1 1
0.4776 0.8196 1
0.5184 1 1
0.2214 0.3545 1
0.5206 1 1
0.4557 1 1
0.4846 1 1
0.4676 0.6677 1
0.3333 0.2722 1
1.4301 1 1
0.4796 0.6642 1
0.3901 0.3894 0.782
0.1688 0.3446 1
0.3444 0.8852 0.8845
0.4676 0.6677 1
0.2214 0.2816 0.3749
1.0447 1 1
0.1682 0.4499 1
0.1682 0.2789 0.2992
1.5681 1 1
0.101632 0.509307 0.736895
0.4776 0.8196 1
0.2768 1 1
0.468 1 1
0.4198 1 1
0.4776 0.8196 1
0.22 0.4051 1
1.531 1 1
0.2066 0.3262 0.9675
1.3973 1 1
1.3843 1 1
0.4776 0.8196 1
0.4751 0.2729 1
1.0531 1 1
0.239 0.5006 1
0.4541 1 1
1.0884 1 1
1.0688 1 1
0.4751 0.2729 1
0.3205 1 0.5
1.4647 1 1
0.7157 1 1
1.4612 1 1
0.4338 1 1
0.4776 0.8196 1
0.3901 0.3894 0.782
1.0537 1 1
0.239 1 1
0.3567 1 1
0.3333 0.2722 1
1.4273 1 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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Gene identifier Rv3793 (Mycobacterium tuberculosis), Integral membrane indolylacetylinositol arabinosyltransferase EmbC (arabinosylindolylacetylinositol synthase)
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