News

The tools CPTP-db and CPTP-Pred have been selected for a talk at miCROPe 2022.

The talk "Genome-wide R-type Tailocin Prediction contributes to low-risk phytosanitary practices"
will be held in session "Microbial biocontrol of pests, pathogens and weeds" on 13 Jul 2022.
Further talks about the application of the PLaBAse and its tools might be presented.

About Us

In collaboration between the University of Tübingen (Algorithms in Bioinformatics), the Leibniz Institute of Vegetable and Ornamental Crops - IGZ Grossbeeren (Beneficial plant-microbe interactions), the Julius Kühn Institute - Federal Research Center for Cultivated Plants (Institute for National and International Plant Health) and the Centre for Plant Biotechnology and Genomics – CBGP Madrid (Phytopathogenic Bacteria) we are continuously establishing novel methods and resources to classify plant-associated microbes among others.

The joint work, is mostly promoted by Sascha Patz (UT), Anupam Gautam (UT & IMPRS-"From Molecules to Organisms", Max Planck Institute for Biology Tübingen), Silke Ruppel (IGZ), Matthias Becker (JKI), Pablo Rodríguez Palenzuela (CBGP), and Daniel H. Huson (UT) and constitutes an initiative to collect current knowledge about plant-associated microbes in one comprehensive web platform. We encourage all researcher around the world to contact us and to share your ideas on how to improve or extend our services.

1. Patz S, Gautam A, Becker M, Ruppel S, Rodríguez-Palenzuela P, Huson DH. PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. (submitted 2021, meanwhile you can read the preprint)
2.Patz S, Gautam A, Becker M, Schrader G, Huson DH. CPTPdb/-Pred: A database and prediction tool for bacterial R-type tailocins and their antagonizing potential against pathogens. (in preparation)
3. Martínez-García PM, López-Solanilla E, Ramos C, Rodríguez-Palenzuela P. Prediction of bacterial associations with plants using a supervised machine-learning approach. Environ Microbiol. 2016 (LINK)
4. Patz S, Becker Y, Richert-Pöggeler KR, Berger B, Ruppel S, Huson DH, Becker M. Phage tail-like particles are versatile bacterial nanomachines – A mini-review. Journal of Advanced Research. 2019 (LINK)
5. Ashrafi S, Kuzmanovic N, Patz S, Lohwasser U, Bunk B, Spröer C, Lorenz M, Frühling A, Neumann-Schaal M, Verbarg S, Becker M, Thünen T. Two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies. (submitted 2022, meanwhile you can read the preprint)
6. Becker Y, Patz S, Werner S, Hoppe B, Feltgen S, Berger B, Schikora A, Glenz R, König S, Erler S, Schrader G, Huson DH, Becker M. Bacteria producing contractile phage tail-like particles (CPTPs) are promising alternatives to conventional chemical pesticides. Journal of Cultivated Plants. 2022 (LINK)

PLEASE CITE THE RESPECTIVE REFERENCES WHEN PUBLISHING ANY RESULT CURATED VIA OUR SERVICES. SEE REFERENCE NUMBERS BELOW EACH SERVICE. THANK YOU!


Services

PLaBA-db

PLaBA-db

Screening for approx. 5,565 plant-assciated bacteria, their plant isolation site, plant interaction phenotype and PGPT annotations, among others.
(CITE REFERENCE 1)

PIFAR-Pred

PIFAR-Pred

Annotation of plant bacterial only interaction factors (proteins) “PIFAR” leads to determination of a plant-associated bacteria, using blastp+hmmer against the PIFAR-BASE.
(CITE REFERENCE 1,3)

PGPT-Pred

PGPT-Pred

Annotation of bacterial plant growth-promoting traits (proteins) "PGPTs" using blastp+hmmer or IMG-KEGG-annoation mapping against the PGPT-BASE.
(CITE REFERENCE 1,5)

CPTP-db

CPTP-db

Screening for potential tailocin encoding bacteria in public datasets and their putative target bacteria based on protein homology.
(CITE REFERENCE 1,2,4,6)
[Access restricted!]

CPTP-Pred

CPTP-Pred

Annotation of potential tailocin syntenic gene clusters and their putative target bacteria based on protein homology, synteny and HMM-Models.
(CITE REFERENCE 1,2,4)
[Access restricted!]

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Version History and Warranty

PLaBAse v.1.02 - Mar 2022
Copyright (C) 2020-2022 Sascha Patz. This web platform and all its services/tools come with ABSOLUTELY NO WARRANTY.
All services (if not restricted) are freely available for ACADEMIC NON-profit institutions, otherwise do not hesitate to contact us by email at plabase[at]inf.uni-tuebingen.de.

Team




Sascha Patz

Author and Tools & Database Curator, University of Tübingen

Anupam Gautam

Website Developer, University of Tübingen

Daniel H. Huson

Prof. (Algorithms in Bioinformatics), University of Tübingen