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ProCarDB: a database of bacterial carotenoids
L N U Nupur1, Asheema Vats2, Sandeep Kumar Dhanda3
1Microbial Type Culture collection and Gene Bank (MTCC), Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India.
BMC Microbiology
|May 28, 2016
Summary
ProCarDB is a new database that compiles information on bacterial carotenoids and their biosynthetic pathways. This resource aids researchers by organizing scattered data on microbial carotenoids, structures, and identification data.
Area of Science:
- Microbiology
- Biochemistry
- Bioinformatics
Background:
- Carotenoids serve critical roles in bacteria, including light harvesting, antioxidant defense, and virulence.
- Existing information on microbial carotenoids is fragmented across scientific literature.
- The post-genomic era has led to a surge in data on carotenoid biosynthesis genes and proteins.
Purpose of the Study:
- To create a centralized, structured, and accessible web resource for microbial carotenoids.
- To consolidate scattered information on bacterial carotenoids and their biosynthetic pathways.
- To provide a valuable tool for researchers in the field of microbial carotenoids.
Main Methods:
- Manual curation of data from published literature and existing databases (KEGG, PubChem, ChEBI, LipidBank, LPSN, UniProt).
- Development of a comprehensive compilation of bacterial carotenoids, named ProCarDB (Prokaryotic Carotenoid Database).
- Integration of data including 2D/3D structures, molecular properties, spectroscopic data (NMR, UV-vis, IR, MS, HPLC), and biosynthetic pathways.
Main Results:
- ProCarDB contains 304 unique carotenoids from 50 biosynthetic pathways in 611 prokaryotes.
- The database includes detailed information on carotenoid structures, molecular formulas, identifiers (SMILES, InChI, KEGG, PubChem, ChEBI), and spectroscopic data.
- Biosynthetic pathways are extended from literature and genomic data, with information on associated genes/enzymes.
Conclusions:
- ProCarDB serves as a comprehensive, open-access repository for bacterial carotenoid information.
- The database facilitates research by integrating diverse data types and providing analysis tools.
- ProCarDB is poised to become a central information hub for scientists studying microbial carotenoids.
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