Journal Article

ProCarDB: a database of bacterial carotenoids

Pinnaka, Anil Kumar, Vats, Asheema, Kumar, Ashwani, Nupur, L. N. U., Dhanda, Sandeep Kumar, Raghava, Gajendra P. S.

2016

Overview

Background Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Results Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Analysis / Bacteria / Bacteria - genetics / Bacterial Proteins - biosynthesis / Bacterial Proteins - chemistry / Biological Microscopy / Biomedical and Life Sciences / Biosynthesis / Biosynthetic Pathways / Carotenoids / Carotenoids - biosynthesis / Carotenoids - chemistry / Data Mining / Databases, Genetic / Dietary supplements / Food / Genes, Bacterial / Genetic code / Genetic engineering / Genomes / Life Sciences / Liquid chromatography / Metabolism / Microbiology / Mycology / Organisms / Oxidizing agents / Parasitology / Physiological aspects / Prevention / Prokaryotes / User-Computer Interface / Virology / Virulence (Microbiology) / Web Browser