Detailed view for Rv3125c

Basic information

TDR Targets ID: 6883
Mycobacterium tuberculosis, PPE family protein PPE49

Source Database / ID:  Tuberculist 

pI: 6.4837 | Length (AA): 391 | MW (Da): 38586 | Paralog Number: 22

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

PF00823   PPE family
PF12484   Polymorphic PE/PPE proteins C terminal

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
3 175 5xfs (B) 1 173 55.00 0 1 0.976355 0.88

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:

  • 2G38:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4KXR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4W4K:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4W4L:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5XFS:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_135481)

Species Accession Gene Product
Mycobacterium tuberculosis Rv3539   PPE family protein PPE63
Mycobacterium tuberculosis Rv2892c   PPE family protein PPE45
Mycobacterium tuberculosis Rv1807   PPE family protein PPE31
Mycobacterium tuberculosis Rv1787   PPE family protein PPE25
Mycobacterium tuberculosis Rv2352c   PPE family protein PPE38
Mycobacterium tuberculosis Rv2770c   PPE family protein PPE44
Mycobacterium tuberculosis Rv3621c   PPE family protein PPE65
Mycobacterium tuberculosis Rv1802   PPE family protein PPE30
Mycobacterium tuberculosis Rv1706c   PPE family protein PPE23
Mycobacterium tuberculosis Rv0915c   PPE family protein PPE14
Mycobacterium tuberculosis Rv1039c   PPE family protein PPE15
Mycobacterium tuberculosis Rv1168c   PPE family protein PPE17
Mycobacterium tuberculosis Rv1705c   PPE family protein PPE22
Mycobacterium tuberculosis Rv1789   PPE family protein PPE26
Mycobacterium tuberculosis Rv1790   PPE family protein PPE27
Mycobacterium tuberculosis Rv1801   PPE family protein PPE29
Mycobacterium tuberculosis Rv1809   PPE family protein PPE33
Mycobacterium tuberculosis Rv2768c   PPE family protein PPE43
Mycobacterium tuberculosis Rv3125c   PPE family protein PPE49
Mycobacterium tuberculosis Rv3136   PPE family protein PPE51
Mycobacterium tuberculosis Rv1808   PPE family protein PPE32
Mycobacterium tuberculosis Rv3532   PPE family protein PPE61
Mycobacterium tuberculosis Rv0388c   PPE family protein PPE9
Mycobacterium ulcerans MUL_3087   PPE family protein
Mycobacterium ulcerans MUL_3074   PPE family protein
Mycobacterium ulcerans MUL_5078   PPE family protein
Mycobacterium ulcerans MUL_2718   PPE family protein
Mycobacterium ulcerans MUL_3089   PPE family protein
Mycobacterium ulcerans MUL_3169   PPE family protein
Mycobacterium ulcerans MUL_2427   PPE family protein
Mycobacterium ulcerans MUL_3076   PPE family protein
Mycobacterium ulcerans MUL_2428   PPE family protein
Mycobacterium ulcerans MUL_2129   PPE family protein
Mycobacterium ulcerans MUL_1702   PPE family protein
Mycobacterium ulcerans MUL_4672   PPE family protein
Mycobacterium ulcerans MUL_3071   PPE family protein
Mycobacterium ulcerans MUL_2167   PPE family protein
Mycobacterium ulcerans MUL_2737   PPE family protein
Mycobacterium ulcerans MUL_4621   PPE family protein
Mycobacterium ulcerans MUL_2094   PPE family protein
Mycobacterium ulcerans MUL_4463   PPE family protein
Mycobacterium ulcerans MUL_1701   PPE family protein
Mycobacterium ulcerans MUL_3072   PPE family protein
Mycobacterium ulcerans MUL_4195   PPE family protein

Essentiality

Rv3125c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu931 Mycobacterium tuberculosis non-essential nmpdr
mtu1056 Mycobacterium tuberculosis non-essential nmpdr
mtu1189 Mycobacterium tuberculosis non-essential nmpdr
mtu1734 Mycobacterium tuberculosis non-essential nmpdr
mtu2815 Mycobacterium tuberculosis non-essential nmpdr
mtu3178 this record Mycobacterium tuberculosis non-essential nmpdr
mtu3593 Mycobacterium tuberculosis non-essential nmpdr
mtu391 Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • 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
  • 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

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv3125c (Mycobacterium tuberculosis), PPE family protein PPE49
Title for this comment
Comment