Detailed view for Rv0355c

Basic information

TDR Targets ID: 6907
Mycobacterium tuberculosis, PPE family protein PPE8
Source Database / ID:  Tuberculist 

pI: 3.9299 | Length (AA): 3300 | MW (Da): 326902 | Paralog Number: 18

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
PF01469   Pentapeptide repeats (8 copies)

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 are 18 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
1 174 5xfs (B) 1 173 55.00 0 1 0.523127 1.16
84 374 4jcl (A) 334 611 28.00 0.82 0.8 0.0747818 1.25
156 471 1czf (A) 36 352 14.00 0 0.05 0.165958 -0.18
229 463 1oa2 (A) 4 218 17.00 0 0.53 0.147412 -0.21
257 440 5ej3 (A) 1 185 16.00 0 0.36 0.222958 -0.79
546 740 3p4g (A) 29 225 33.00 0.0012 0.52 0.273691 -0.61
1511 1698 1igo (A) 7 201 16.00 0 0.37 0.16317 -0.49
1525 1717 2vgd (A) 4 190 18.00 0 0.41 0.228685 -0.5
1533 1694 1xnd (A) 6 184 28.00 0.7 0.29 0.189691 -0.2
1845 2089 3pr7 (A) 86 311 32.00 0.0043 0.05 0.111842 0.89
2024 2167 3fhv (A) 32 178 18.00 0 0.08 0.217836 -1.08
2025 2209 2nqy (A) 6 199 15.00 0 0.07 0.111261 -0.5
2377 2483 4yc5 (A) 59 170 36.00 0.016 0.65 0.546024 -1.37
2388 2475 2j8i (A) 10 97 27.00 0 0.86 0.424867 -1.23
2555 3195 5n8p (A) 259 950 28.00 0.0000000014 0.63 0.293842 0.75
3071 3268 3b90 (A) 136 343 12.00 0 0.17 0.1642 -0.96
3099 3289 3wx5 (A) 41 237 12.00 0 0.05 0.137079 -0.76
3119 3269 3ml3 (A) 587 724 14.00 0 0.06 0.0979576 -0.84

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
  • 5XFS:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
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_132376)

Species Accession Gene Product
Babesia bovis BBOV_II003500   hypothetical protein
Mycobacterium tuberculosis Rv0442c   PPE family protein PPE10
Mycobacterium tuberculosis Rv2356c   PPE family protein PPE40
Mycobacterium tuberculosis Rv3144c   PPE family protein PPE52
Mycobacterium tuberculosis Rv0755c   PPE family protein PPE12
Mycobacterium tuberculosis Rv0878c   PPE family protein PPE13
Mycobacterium tuberculosis Rv1135c   PPE family protein PPE16
Mycobacterium tuberculosis Rv1548c   PPE family protein PPE21
Mycobacterium tuberculosis Rv1753c   PPE family protein PPE24
Mycobacterium tuberculosis Rv1917c   PPE family protein PPE34
Mycobacterium tuberculosis Rv1918c   PPE family protein PPE35
Mycobacterium tuberculosis Rv2353c   PPE family protein PPE39
Mycobacterium tuberculosis Rv0304c   PPE family protein PPE5
Mycobacterium tuberculosis Rv3159c   PPE family protein PPE53
Mycobacterium tuberculosis Rv3343c   PPE family protein PPE54
Mycobacterium tuberculosis Rv3347c   PPE family protein PPE55
Mycobacterium tuberculosis Rv3350c   PPE family protein PPE56
Mycobacterium tuberculosis Rv0305c   PPE family protein PPE6
Mycobacterium tuberculosis Rv3558   PPE family protein PPE64
Mycobacterium tuberculosis Rv0355c   PPE family protein PPE8
Mycobacterium ulcerans MUL_0098   PPE family protein
Mycobacterium ulcerans MUL_1395   PPE family protein
Mycobacterium ulcerans MUL_0890   PPE family protein
Mycobacterium ulcerans MUL_0782   PPE family protein
Mycobacterium ulcerans MUL_0902   PPE family protein
Mycobacterium ulcerans MUL_0965   PPE family protein
Mycobacterium ulcerans MUL_0964   PPE family protein
Mycobacterium ulcerans MUL_4491   PPE family protein
Plasmodium falciparum PF3D7_0201900   erythrocyte membrane protein 3

Essentiality

Rv0355c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu769 Mycobacterium tuberculosis essential nmpdr
mtu894 Mycobacterium tuberculosis non-essential nmpdr
mtu1155 Mycobacterium tuberculosis non-essential nmpdr
mtu1783 Mycobacterium tuberculosis essential nmpdr
mtu1948 Mycobacterium tuberculosis non-essential nmpdr
mtu1949 Mycobacterium tuberculosis non-essential nmpdr
mtu307 Mycobacterium tuberculosis non-essential nmpdr
mtu3403 Mycobacterium tuberculosis essential nmpdr
mtu308 Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

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.

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User comments

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Gene identifier Rv0355c (Mycobacterium tuberculosis), PPE family protein PPE8
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