Detailed view for Rv3508

Basic information

TDR Targets ID: 6710
Mycobacterium tuberculosis, PE-PGRS family protein PE_PGRS54
Source Database / ID:  Tuberculist 

pI: 3.5385 | Length (AA): 1901 | MW (Da): 147625 | Paralog Number: 49

Signal peptide: Y | 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

PF00934   PE family

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 7 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
8 84 5xfs (A) 8 84 47.00 0.0000001 0.12 0.460305 0.56
213 242 2kh2 (B) 110 139 53.00 0.35 0.2 0.426581 1.33
226 301 2pne (A) 6 81 43.00 0.018 0.2 0.415979 0.49
480 569 2pne (A) 3 80 58.00 0.00000000022 0.95 0.572143 -0.06
535 613 2pne (A) 3 80 44.00 0 0.83 0.622757 -1.01
1768 1880 6f45 (D) 114 235 43.00 0.00000072 0.91 0.514242 -0.7
1770 1813 3bog (C) 3 79 76.00 0.0000021 0.19 0.640946 -0.25

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 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_129879)

Species Accession Gene Product
Mycobacterium tuberculosis Rv0109   PE-PGRS family protein PE_PGRS1
Mycobacterium tuberculosis Rv0747   PE-PGRS family protein PE_PGRS10
Mycobacterium tuberculosis Rv0754   PE-PGRS family protein PE_PGRS11
Mycobacterium tuberculosis Rv0833   PE-PGRS family protein PE_PGRS13
Mycobacterium tuberculosis Rv0834c   PE-PGRS family protein PE_PGRS14
Mycobacterium tuberculosis Rv0872c   PE-PGRS family protein PE_PGRS15
Mycobacterium tuberculosis Rv0978c   PE-PGRS family protein PE_PGRS17
Mycobacterium tuberculosis Rv0980c   PE-PGRS family protein PE_PGRS18
Mycobacterium tuberculosis Rv1067c   PE-PGRS family protein PE_PGRS19
Mycobacterium tuberculosis Rv0124   PE-PGRS family protein PE_PGRS2
Mycobacterium tuberculosis Rv1068c   PE-PGRS family protein PE_PGRS20
Mycobacterium tuberculosis Rv1087   PE-PGRS family protein PE_PGRS21
Mycobacterium tuberculosis Rv1091   PE-PGRS family protein PE_PGRS22
Mycobacterium tuberculosis Rv1243c   PE-PGRS family protein PE_PGRS23
Mycobacterium tuberculosis Rv1325c   PE-PGRS family protein PE_PGRS24
Mycobacterium tuberculosis Rv1396c   PE-PGRS family protein PE_PGRS25
Mycobacterium tuberculosis Rv1441c   PE-PGRS family protein PE_PGRS26
Mycobacterium tuberculosis Rv1450c   PE-PGRS family protein PE_PGRS27
Mycobacterium tuberculosis Rv1452c   PE-PGRS family protein PE_PGRS28
Mycobacterium tuberculosis Rv1468c   PE-PGRS family protein PE_PGRS29
Mycobacterium tuberculosis Rv0278c   PE-PGRS family protein PE_PGRS3
Mycobacterium tuberculosis Rv1768   PE-PGRS family protein PE_PGRS31
Mycobacterium tuberculosis Rv1818c   PE-PGRS family protein PE_PGRS33
Mycobacterium tuberculosis Rv1840c   PE-PGRS family protein PE_PGRS34
Mycobacterium tuberculosis Rv2162c   PE-PGRS family protein PE_PGRS38
Mycobacterium tuberculosis Rv2340c   PE-PGRS family protein PE_PGRS39
Mycobacterium tuberculosis Rv0279c   PE-PGRS family protein PE_PGRS4
Mycobacterium tuberculosis Rv2396   PE-PGRS family protein PE_PGRS41
Mycobacterium tuberculosis Rv2487c   PE-PGRS family protein PE_PGRS42
Mycobacterium tuberculosis Rv2490c   PE-PGRS family protein PE_PGRS43
Mycobacterium tuberculosis Rv2591   PE-PGRS family protein PE_PGRS44
Mycobacterium tuberculosis Rv2615c   PE-PGRS family protein PE_PGRS45
Mycobacterium tuberculosis Rv2634c   PE-PGRS family protein PE_PGRS46
Mycobacterium tuberculosis Rv2741   PE-PGRS family protein PE_PGRS47
Mycobacterium tuberculosis Rv2853   PE-PGRS family protein PE_PGRS48
Mycobacterium tuberculosis Rv1759c   PE-PGRS family protein Wag22
Mycobacterium tuberculosis Rv3345c   PE-PGRS family protein PE_PGRS50
Mycobacterium tuberculosis Rv3367   PE-PGRS family protein PE_PGRS51
Mycobacterium tuberculosis Rv3388   PE-PGRS family protein PE_PGRS52
Mycobacterium tuberculosis Rv3507   PE-PGRS family protein PE_PGRS53
Mycobacterium tuberculosis Rv3508   PE-PGRS family protein PE_PGRS54
Mycobacterium tuberculosis Rv3511   PE-PGRS family protein PE_PGRS55
Mycobacterium tuberculosis Rv3514   PE-PGRS family protein PE_PGRS57
Mycobacterium tuberculosis Rv3590c   PE-PGRS family protein PE_PGRS58
Mycobacterium tuberculosis Rv3595c   PE-PGRS family protein PE_PGRS59
Mycobacterium tuberculosis Rv0532   PE-PGRS family protein PE_PGRS6
Mycobacterium tuberculosis Rv0578c   PE-PGRS family protein PE_PGRS7
Mycobacterium tuberculosis Rv0746   PE-PGRS family protein PE_PGRS9
Mycobacterium tuberculosis Rv3390   Probable conserved lipoprotein LpqD
Mycobacterium tuberculosis Rv1983   PE-PGRS family protein PE_PGRS35
Mycobacterium ulcerans MUL_2702   PE-PGRS family protein
Mycobacterium ulcerans MUL_0919   lipoprotein LpqD
Mycobacterium ulcerans MUL_1870   PE-PGRS family protein
Mycobacterium ulcerans MUL_3982   PE-PGRS family protein
Mycobacterium ulcerans MUL_1639   PE-PGRS family protein
Mycobacterium ulcerans MUL_3440   hypothetical protein
Mycobacterium ulcerans MUL_2395   PE family protein
Mycobacterium ulcerans MUL_3975   PE-PGRS family protein

Essentiality

Rv3508 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3450 Mycobacterium tuberculosis non-essential nmpdr
mtu760 Mycobacterium tuberculosis non-essential nmpdr
mtu768 Mycobacterium tuberculosis non-essential nmpdr
mtu888 Mycobacterium tuberculosis non-essential nmpdr
mtu1084 Mycobacterium tuberculosis non-essential nmpdr
mtu1264 Mycobacterium tuberculosis non-essential nmpdr
mtu1348 Mycobacterium tuberculosis non-essential nmpdr
mtu1419 Mycobacterium tuberculosis non-essential nmpdr
mtu1464 Mycobacterium tuberculosis non-essential nmpdr
mtu1491 Mycobacterium tuberculosis non-essential nmpdr
mtu1848 Mycobacterium tuberculosis non-essential nmpdr
mtu1870 Mycobacterium tuberculosis non-essential nmpdr
mtu2196 Mycobacterium tuberculosis non-essential nmpdr
mtu2381 Mycobacterium tuberculosis non-essential nmpdr
mtu2437 Mycobacterium tuberculosis non-essential nmpdr
mtu2635 Mycobacterium tuberculosis non-essential nmpdr
mtu2661 Mycobacterium tuberculosis non-essential nmpdr
mtu2680 Mycobacterium tuberculosis non-essential nmpdr
mtu2900 Mycobacterium tuberculosis non-essential nmpdr
mtu3427 Mycobacterium tuberculosis non-essential nmpdr
mtu3568 Mycobacterium tuberculosis non-essential nmpdr
mtu3652 Mycobacterium tuberculosis non-essential nmpdr
mtu3657 Mycobacterium tuberculosis non-essential nmpdr
mtu586 Mycobacterium tuberculosis non-essential nmpdr
mtu1789 Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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

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): 0.5

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.

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Gene identifier Rv3508 (Mycobacterium tuberculosis), PE-PGRS family protein PE_PGRS54
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