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Published on: March 11, 2017
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PVCbase: an integrated web resource for the PVC bacterial proteomes
Nicola Bordin1, Juan Carlos González-Sánchez2,3, Damien P Devos1
1Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, Seville 41013, Spain.
Summary
A new web resource, PVCbase, now integrates in silico predictions for the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. This resource aids researchers by consolidating protein function and structure data for these important microbes.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- The Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum is of increasing research interest.
- A dedicated, integrated web resource for in silico predictions for PVC organisms was lacking.
Purpose of the Study:
- To develop and present PVCbase, a specialized web resource for the PVC bacterial superphylum.
- To provide an integrated platform for in silico predictions, including protein function and structure.
Main Methods:
- Integration of protein function annotations and tertiary structure predictions for 39 representative PVC proteomes (PVCdb).
- Development of a protein feature visualizer (Foundation) and a custom BLAST webserver (PVCBlast).
- Inclusion of results from diverse prediction tools covering multiple functional aspects.
Main Results:
- PVCbase offers a comprehensive overview of protein identities through integrated data.
- The resource facilitates direct retrieval of annotations via the PVCBlast webserver.
- Demonstration of PVCdb's utility in addressing biological questions using raw data.
Conclusions:
- PVCbase serves as a valuable, integrated hub for researchers studying the PVC bacterial superphylum.
- The resource enhances the understanding of PVC organism proteomes through consolidated in silico predictions.
- PVCbase is freely accessible, promoting wider research and discovery in the field.
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