Detailed view for MUL_3508

Basic information

TDR Targets ID: 953787
Mycobacterium ulcerans, penicillin-binding membrane protein PbpB
Source Database / ID:  KEGG  

pI: 9.9816 | Length (AA): 691 | MW (Da): 74155 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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
PF03717   Penicillin-binding Protein dimerisation domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008658   penicillin binding  

Metabolic Pathways

Peptidoglycan biosynthesis (KEGG)
beta-Lactam resistance (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
7 203 1z69 (A) 126 325 14.00 0 0.28 0.316494 -0.12
112 676 1vqq (A) 116 666 17.00 0 1 0.847056 0.42
135 683 5df7 (A) 50 562 33.00 0 1 1.1775 -0.32
324 679 5uy7 (A) 233 568 37.00 0 1 0.916195 -0.8

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_131512)

Species Accession Gene Product
Chlamydia trachomatis CT_270   transglycolase/transpeptidase
Escherichia coli b0084   transpeptidase involved in septal peptidoglycan synthesis (penicillin-binding protein 3)
Mycobacterium leprae ML0908   Probable penicillin-binding membrane protein PbpB
Mycobacterium tuberculosis Rv2163c   Probable penicillin-binding membrane protein PbpB
Mycobacterium ulcerans MUL_3508   penicillin-binding membrane protein PbpB
Schmidtea mediterranea mk4.086392.00  
Treponema pallidum TP0760   penicillin-binding protein (pbp-3)

Essentiality

MUL_3508 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0084 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Pseudomonas aeruginosa Penicillin-binding protein 3 Compounds References
Staphylococcus aureus Penicillin-binding protein 1 Compounds References
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) Penicillin-binding protein 2x 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
0.1418 0.8607 1
0.075 0.588 0.879
0.0295 0.7103 1
0.1423 0.8981 1
0.053 0.6057 0.9955
0.1562 0.8633 1
0.1467 0.6996 1
0.0651 0.9315 1
0.0708 0.4899 1
0.0698 0.3298 1
0.0661 0.5621 0.8832
0.0748 0.2965 1
0.0615 0.2658 0.6062
0.0223 0.3665 0.297
0.0548 0.5933 1
0.1349 0.444 0.4481
0.1704 0.2501 0.6853
0.0656 0.9962 1
0.021 0.3867 0.3809
0.1621 0.8982 1
0.1482 0.8632 1
0.0749 0.2836 0.879
0.0704 0.588 0.879
0.1462 0.8626 1
0.1586 0.8635 1
0.0651 0.9962 1
0.0665 0.9962 1
0.0848 0.3899 1
0.1441 0.6103 1
0.0275 0.3974 0.3809
0.0687 0.588 0.879
0.0748 0.2965 1
0.0698 0.3298 1
0.0615 0.9962 1
0.2297 0.8923 1
0.0616 0.9963 1
0.1503 0.7223 1
0.0799 0.4053 1
0.0602 0.7712 1
0.3009 0.8621 1
0.1497 0.7226 1
0.0593 0.7677 1
0.0638 0.3348 1
0.0699 0.588 0.879
0.32 0.8815 1
0.031 0.314 0.3433
0.1644 0.9024 1
0.0387 0.3572 0.6348
0.1603 0.8592 1
0.1599 0.8138 1
0.1466 0.4288 1
0.0211 0.3793 0.3809
0.0641 0.9962 1
0.161 0.281 1
0.0616 0.9963 1
0.0824 0.5899 0.8833
0.0168 0.3948 0.3809
0.0529 0.4011 1
0.0528 0.5564 1
0.3259 0.274 1
0.1024 0.2608 0.2593
0.0848 0.3899 1
0.0848 0.3899 1
0.1547 0.9032 1
0.0622 0.9962 1
0.0602 0.4339 0.6441
0.1626 0.7651 1
0.0821 0.776 1
0.0298 0.4349 0.3809
0.138 0.8714 1
0.3259 0.2574 1
0.1644 0.9024 1
0.0691 0.5863 0.8816
0.075 0.4909 1
0.0824 0.348 0.6487
0.0653 0.3042 1
0.0824 0.5899 0.8833
0.1538 0.8625 1
0.0649 0.901 0.901
0.22 0.8983 1
0.0721 0.4909 1
0.0665 0.588 0.879
0.0567 0.7689 1
0.0245 0.3522 0.297
0.1466 0.4288 1
0.1667 0.3577 1
0.0306 0.366 0
0.0641 0.9962 1
0.1466 0.4288 1
0.068 0.588 0.879
0.0848 0.3899 1
0.0616 0.9963 1
0.1533 0.2599 1
0.0662 0.9963 1
0.1547 0.4441 0.4502
0.0748 0.502 1
0.2891 0.5192 0.5185
0.0808 0.4525 1
0.0654 0.9962 1
0.1167 0.4441 0.3809
0.0714 0.588 0.879
0.1543 0.8629 1
0.1498 0.4448 0.3809
0.1532 0.8629 1
0.0672 0.407 1
0.0687 0.588 0.879
0.1288 0.3151 0
0.0319 0.4259 0.3809
0.1634 0.8735 1
0.0655 0.9962 1
0.066 0.6429 1
0.0806 0.772 1
0.0641 0.9962 1
0.2748 0.274 1
0.2264 0.899 1
0.0635 0.9962 1
0.0808 0.4525 1
0.0154 0.3747 0.3156
0.066 0.9962 1
0.1498 0.8624 1
0.1667 0.3577 1
0.1477 0.8611 1
0.1466 0.4288 1
0.0653 0.5028 1
0.1288 0.3151 0
0.2297 0.8923 1
0.2766 0.8621 1
0.0201 0.5908 1
0.107 0.4454 0.4508
0.0529 0.4011 1
0.1325 0.6375 1
0.0319 0.4259 0.3809
0.146 0.2607 1
0.1579 0.8625 1
0.1422 0.8933 1
0.0626 0.3805 1
0.0641 0.9962 1
0.1467 0.8625 1
0.161 0.281 1
0.0807 0.6327 0.7542
0.161 0.281 1
0.0614 0.9962 1
0.062 0.9962 1
0.1409 0.8849 1
0.1428 0.8598 1
0.0627 0.4314 0.6395
0.1337 0.6667 0.6487
0.1423 0.8981 1
0.1594 0.8137 1
0.1423 0.8981 1
0.1533 0.2599 1
0.0674 0.9963 1
0.0806 0.772 1
0.0664 0.588 0.879
0.0665 0.9962 1
0.1321 0.8714 1
0.1423 0.8981 1
0.0168 0.3682 0
0.0138 0.2539 0
0.0292 0.3273 0
0.0665 0.9962 1
0.0138 0.363 0.3222
0.0661 0.5621 0.8832
0.1551 0.898 1
0.031 0.2976 0
0.0276 0.3628 0
0.0482 0.6054 0.6348
0.0374 0.6391 1
0.0656 0.9962 1
0.0798 0.7693 1
0.0463 0.7712 1
0.1418 0.8607 1
0.0662 0.9963 1
0.1704 0.2501 0.6853
0.146 0.2607 1
0.0615 0.2658 0.6062
0.0687 0.588 0.879
0.1515 0.8633 1
0.0245 0.3763 0.3763
0.0824 0.5899 0.8833
0.1704 0.2501 0.6853
0.3198 0.5799 0.7336
0.0665 0.9962 1
0.0804 0.7674 1
0.1347 0.4378 0.441
0.1531 0.8597 1
0.1579 0.8639 1
0.1559 0.9024 1
0.0618 0.9962 1
0.223 0.8967 1
0.1392 0.8936 1
0.1632 0.7091 0.8379
0.0629 0.5144 1
0.1533 0.2599 1
0.146 0.2607 1
0.0649 0.7712 1
0.1389 0.8915 1
0.0838 0.7772 1
0.1329 0.4428 0.4479
0.0615 0.2658 0.6062
0.0636 0.7676 1
0.021 0.3867 0.3809
0.1704 0.2501 0.6853
0.0688 0.588 0.8813
0.0824 0.5899 0.8833
0.0687 0.588 0.879
0.0653 0.2673 1
0.0155 0.2942 0.2795
0.1479 0.8619 1
0.0665 0.9962 1
0.0848 0.3899 1
0.0622 0.9962 1
0.1698 0.8129 1
0.156 0.8885 1
0.0661 0.588 0.879
0.0641 0.9962 1
0.2869 0.8578 1
0.0815 0.588 0.879
0.0679 0.588 0.879
0.0558 0.6213 0.6761
0.0154 0.3747 0.3156
0.1826 0.8805 1
0.0718 0.4886 1
0.0681 0.9962 1
0.1336 0.4427 0.4489
0.0293 0.4007 0.3809
0.1392 0.8936 1
0.132 0.8144 1
0.1482 0.8637 1
0.0993 0.7718 1
0.0622 0.7678 1
0.0848 0.3899 1
0.1462 0.5216 1
0.0542 0.771 1
0.0633 0.9962 1
0.146 0.2607 1
0.1466 0.4288 1
0.1446 0.8914 1
0.067 0.5887 0.879
0.0713 0.588 0.879
0.1464 0.8972 1
0.1462 0.8626 1
0.0138 0.2539 0
0.0709 0.4528 0.879
0.1548 0.866 1
0.0798 0.7693 1
0.0714 0.3199 0.8808
0.0217 0.3872 0.3809
0.1754 0.8767 1
0.2255 0.899 1
0.1466 0.8633 1
0.0709 0.4528 0.879
0.0635 0.9962 1
0.1338 0.8766 0.8716
0.1595 0.5069 1
0.0665 0.9962 1
0.2239 0.8967 1
0.1024 0.2608 0.2593
0.0708 0.4899 1
0.0674 0.4138 1
0.1547 0.4441 0.4502
0.0635 0.9962 1
0.0665 0.9962 1
0.1574 0.8634 1
0.0848 0.3899 1
0.0723 0.4906 1
0.0627 0.4326 1
0.1579 0.8625 1
0.1625 0.7071 1
0.1354 0.8714 1
0.1438 0.8604 1
0.1564 0.3942 0.3809
0.1378 0.8714 1
0.0532 0.7671 1
0.117 0.4441 0.3809
0.1482 0.863 1
0.0551 0.6214 1
0.0532 0.6065 1
0.1343 0.2624 0.4418
0.066 0.9962 1
0.0746 0.502 1
0.1206 0.4075 1
0.0671 0.2506 1
0.0656 0.9962 1
0.1418 0.8607 1
0.0687 0.588 0.879
0.0838 0.7772 1
0.1754 0.8767 1
0.0639 0.9963 1
0.0744 0.588 0.879
0.1456 0.8627 1
0.0791 0.588 0.879
0.1547 0.4441 0.4502
0.0848 0.3899 1
0.1547 0.4441 0.4502
0.0768 0.9963 1
0.066 0.9962 1
0.1562 0.8633 1
0.0784 0.5887 0.879
0.0168 0.3682 0
0.143 0.8908 1
0.0719 0.4909 1
0.0564 0.7712 1
0.1533 0.2599 1
0.0745 0.35 0.8824
0.0686 0.4905 1
0.1552 0.8617 1
0.1441 0.6103 1
0.0756 0.4912 1
0.1423 0.8981 1
0.0665 0.9962 1
0.0665 0.9962 1
0.1024 0.2608 0.2593
0.0698 0.3298 1
0.0653 0.3042 1
0.3317 0.8815 1
0.0655 0.9962 1
0.3855 0.344 0.571
0.0734 0.489 1
0.0651 0.9315 1
0.2269 0.8988 1
0.0708 0.4899 1
0.1449 0.857 1
0.0126 0.9962 1
0.1626 0.7651 1
0.1466 0.8633 1
0.1503 0.7223 1
0.1429 0.8586 1
0.2281 0.8967 1
0.0797 0.4087 0.8744
0.0725 0.5894 0.879
0.0569 0.3916 0.6633
0.1516 0.422 0.3809
0.161 0.281 1
0.1462 0.8626 1
0.2201 0.8732 1
0.0641 0.9962 1
0.1515 0.8976 1
0.0527 0.5778 1
0.0615 0.2658 0.6062
0.0245 0.364 0.297
0.1482 0.8629 1
0.1273 0.3944 0.3941
0.1441 0.6103 1
0.0303 0.3512 0
0.1346 0.668 0.662
0.1661 0.6916 1
0.0627 0.4314 0.6395
0.0709 0.4528 0.879
0.0656 0.7681 1
0.0618 0.9962 1
0.1483 0.8622 1
0.0681 0.9962 1
0.0658 0.9962 1
0.0787 0.588 0.879
0.0649 0.901 0.901
0.0641 0.9962 1
0.068 0.5887 0.8817
0.1533 0.2599 1
0.0793 0.7674 1
0.08 0.7752 1
0.0708 0.4899 1
0.1024 0.2608 0.2593
0.0653 0.5028 1
0.0202 0.2625 0
0.0686 0.4905 1
0.1482 0.863 1
0.1789 0.7915 1
0.0684 0.9962 1
0.0674 0.4138 1
0.0698 0.9962 1
0.0653 0.2673 1
0.0807 0.6327 0.7542
0.0558 0.6213 0.6761
0.0665 0.588 0.879
0.1138 0.3072 0.4612
0.0674 0.9963 1
0.1462 0.5216 1
0.1445 0.8624 1
0.1594 0.8693 1
0.1509 0.8629 1
0.0736 0.4909 1
0.2207 0.8167 1
0.0808 0.4525 1
0.2504 0.274 1
0.1336 0.4427 0.4489
0.1528 0.8976 1
0.0214 0.4099 0.5196
0.0665 0.588 0.879
0.0665 0.9962 1
0.0665 0.9962 1
0.0824 0.5899 0.8833
0.2748 0.274 1
0.0808 0.4525 1
0.1024 0.2608 0.2593
0.1264 0.4513 0.4527
0.0615 0.2658 0.6062
0.1445 0.8624 1
0.0672 0.407 1
0.08 0.7752 1
0.0671 0.2506 1
0.1605 0.8641 1
0.0817 0.7675 1
0.1503 0.7223 1
0.0665 0.588 0.879
0.0615 0.9963 1
0.1189 0.4456 0.4416
0.0284 0.3439 0
0.0536 0.771 1
0.1539 0.8626 1
0.0615 0.2658 0.6062
0.1467 0.6996 1
0.2207 0.8167 1
0.0667 0.9962 1
0.1343 0.2624 0.4418
0.0413 0.297 0.297
0.0668 0.7656 1
0.146 0.2607 1
0.0674 0.4138 1
0.1467 0.8625 1
0.0677 0.588 0.879
0.1485 0.8979 1
0.1441 0.8611 1
0.0804 0.7675 1
0.1826 0.8805 1
0.0284 0.3439 0
0.1447 0.8611 1
0.0672 0.407 1

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 MUL_3508 (Mycobacterium ulcerans), penicillin-binding membrane protein PbpB
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