Detailed view for Rv2864c

Basic information

TDR Targets ID: 8815
Mycobacterium tuberculosis, Possible penicillin-binding lipoprotein
Source Database / ID:  Tuberculist 

pI: 5.7363 | Length (AA): 603 | MW (Da): 63014 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF00905   Penicillin binding protein transpeptidase domain
PF05223   NTF2-like N-terminal transpeptidase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008658   penicillin binding  
GO:0046677   response to antibiotic  
GO:0009273   peptidoglycan-based cell wall biogenesis  

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
26 601 5e31 (A) 39 677 20.00 0 1 1.08932 0.35
243 599 4r3j (A) 547 946 27.00 0 1 0.81014 -0.29
275 566 4mnr (A) 61 413 32.00 0 1 0.675645 0.38
302 600 5crf (A) 281 606 24.00 0 1 0.696954 -0.42

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. 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_237708)

Species Accession Gene Product
Mycobacterium leprae ML1577c   POSSIBLE PENICILLIN-BINDING LIPOPROTEIN
Mycobacterium tuberculosis Rv2864c   Possible penicillin-binding lipoprotein
Mycobacterium ulcerans MUL_2089   penicillin-binding lipoprotein

Essentiality

Rv2864c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
this record Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0371 0.2851 1
0.0375 0.8048 1
0.3453 0.985 1
0.0391 0.3168 1
0.0371 0.9844 1
0.0391 0.3168 1
0.0686 0.2945 0.6515
0.0441 0.3117 0.9121
0.0704 0.3676 0.6578
0.254 0.4206 0.4206
0.0479 0.3192 0.9121
0.2261 0.5857 0.5853
0.2454 0.6661 1
0.0692 0.976 1
0.0319 0.9588 1
0.0462 0.312 0.9121
0.0297 0.3798 1
0.254 0.4206 0.4206
0.0731 0.3557 0.6242
0.0455 0.3108 0.9121
0.0457 0.4026 1
0.0647 0.9852 1
0.0319 0.9588 1
0.2363 0.9863 1
0.254 0.4206 0.4206
0.2975 0.9861 1
0.0768 0.2999 0.5327
0.0697 0.349 0.628
0.0711 0.3285 0.6284
0.0387 0.7898 1
0.254 0.4206 0.4206
0.1293 0.5482 1
0.1293 0.5482 1
0.0569 0.2697 0.7784
0.0731 0.3557 0.6242
0.0726 0.2986 0.6304
0.0676 0.9843 1
0.0951 0.3527 0.7245
0.0577 0.3515 0.6301
0.2914 0.9753 1
0.1313 0.3745 0.7325
0.0752 0.3036 0.539
0.254 0.4206 0.4206
0.0471 0.311 0.9121
0.0803 0.316 0.5636
0.2261 0.5857 0.5853
0.0685 0.2861 1
0.0371 0.4394 1
0.0689 0.2953 0.4541
0.0455 0.3108 0.9121
0.0371 0.4388 1
0.0297 0.3798 1
0.0341 0.9846 1
0.0781 0.3096 0.5512
0.0668 0.984 1
0.254 0.4206 0.4206
0.295 0.9862 1
0.0375 0.8048 1
0.0461 0.3104 0.9121
0.0129 0.3089 0.8676
0.3348 0.9857 1
0.0554 0.3194 0.5622
0.1174 0.431 0.7851
0.0371 0.458 1
0.3308 0.9863 1
0.0335 0.5631 1
0.1293 0.5482 1
0.295 0.9862 1
0.063 0.9588 1
0.0661 0.9753 1
0.0305 0.9816 1
0.038 0.7854 1
0.0424 0.3959 0.9055
0.1174 0.431 0.7851
0.3941 0.7089 1
0.0704 0.9858 1
0.0621 0.2944 0.6318
0.0788 0.3087 0.573
0.0891 0.2542 0.4554
0.0676 0.9495 1
0.3416 0.9863 1
0.3634 0.2962 1
0.0621 0.2944 0.6318
0.0743 0.3473 0.6096
0.0371 0.4105 1
0.0463 0.3122 0.9121
0.0807 0.3161 0.5641
0.0391 0.3168 1
0.0717 0.3789 0.6421
0.2844 0.9831 1
0.0588 0.3139 0.5577
0.2844 0.9831 1
0.0335 0.5631 1
0.0743 0.3473 0.6096
0.0799 0.3096 0.5512
0.0658 0.986 1
0.0558 0.3139 0.5577
0.0513 0.2574 0.9121
0.0785 0.301 0.5336
0.0464 0.3117 0.9121
0.4346 0.7897 1
0.1293 0.5482 1
0.0739 0.3838 0.6645
0.254 0.4206 0.4206
0.3416 0.9863 1
0.0729 0.3853 0.6609
0.2727 0.9864 1
0.254 0.4206 0.4206
0.1215 0.3599 0.7029
0.0305 0.9816 1
0.2786 0.9753 1
0.254 0.4206 0.4206
0.0455 0.3108 0.9121
0.0619 0.2952 0.6318
0.0684 0.9826 1
0.067 0.981 1
0.0371 0.9753 1
0.2935 0.9862 1
0.0621 0.2944 0.6318
0.0742 0.3461 0.6234
0.0704 0.9858 1
0.2584 0.9863 1
0.2261 0.5857 0.5853
0.0645 0.9834 1
0.0607 0.9851 1
0.0588 0.3139 0.5577
0.1243 0.3398 0.655
0.0482 0.3122 0.9121
0.0376 0.7884 1
0.0629 0.3892 0.7917
0.3686 0.9588 1
0.0784 0.3096 0.5447
0.2577 0.9863 1
0.0371 0.599 1
0.0455 0.3108 0.9121
0.0429 0.4063 0.8711
0.061 0.3461 0.618
0.0785 0.301 0.5336
0.0371 0.9844 1
0.2966 0.581 1
0.061 0.9843 1
0.0335 0.5631 1
0.2261 0.5857 0.5853
0.0485 0.3125 0.9121
0.0628 0.9838 1
0.2966 0.581 1
0.3416 0.9863 1
0.254 0.4206 0.4206
0.2979 0.9863 1
0.0441 0.3117 0.9121
0.0341 0.9846 1
0.038 0.4659 1
0.0371 0.985 1
0.0699 0.3495 0.6286
0.1207 0.3745 0.7324
0.048 0.3192 0.9121
0.2261 0.5857 0.5853
0.0628 0.9838 1
0.0717 0.3789 0.6421
0.3416 0.9863 1
0.0214 0.563 1
0.3686 0.9588 1
0.1289 0.3395 0.6547
0.2337 0.7253 0.9718
0.0335 0.5631 1
0.0473 0.3122 0.9121
0.0711 0.3285 0.6284

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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Gene identifier Rv2864c (Mycobacterium tuberculosis), Possible penicillin-binding lipoprotein
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