Ans:ProCarDB is a comprehensive compilation of information pertaining to prokaryotic carotenoids. It contains more than 1900 entries. The entries have been included manually extracted data from more than 2000 articles listed in Pubmed, Google Scholar, Science Direct and IJSEM. The extracted data if further supplemented with the relevant information available in important databases such as KEGG, PubChem, LSPN etc. Each entry provides important information about:
1. Carotenoid details such as structure, carotenoid name, molecular weight, molecular formula, relevant molecular properties for identification and characterization, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, ChEBI id etc.
2. Also, information regarding pathways involved in the synthesis of carotenoids, enzymes, encoding genes, bacterial species possessing carotenoids.
3. This database is assisted with various online tools that allow the user to retrieve and analyze data, search for similar carotenoids and homologues genes/proteins.
Q: Unique features of ProCarDB?
Ans: The following are the unique features of ProCarDB.
1. ProCarDB is the only freely accessible, comprehensive database on microbial carotenoids.
2. Provides details of Pathways involved in the carotenoid biosynthesis along with encoding genes/operons.
3. At least 15 such pathways are not described in popular databases such as KeGG.
4. Genes of carotenoids has been fished out from the whole genome data submitted in GenBank. Based on the genes identification, pathways and carotenoids prediction has also been performed.
5. The database provide important details on carotenoids like IUPAC notation, sys-name, or other names known; molecular weight, molecular formula, relevant molecular properties for identification and characterization. Hence this data can also help the viewer in identification and characterization of carotenoids.
Q: Does ProCarDB represent all known carotenoids from the prokaryotic Domain?
Ans:To the best of our knowledge, ProCarDB is the largest, freely available, comprehensive compilation of experimentally characterized prokaryotic carotenoids described in the published literature and from publically available databases. The database is comprised of all known bacterial carotenoids till October 2015. Every possible effort was made to incorporate all the available data on prokaryotic carotenoids and thus represents a comprehensive collection, however by no means, we claim that the ProCarDB contain all the available information on prokaryotic carotenoids. Furthermore, we encourage users to refer to the original literature for more information.
Q: Future Plans for ProCarDB
Ans:We plan to update our data after every six months based on information extracted from the newly published literature or from the data that submitted to us through ProCarDB. We will further update the information on the genes involved in carotenoid biosynthesis through annotation of newly sequenced genomes.
Q: Can I search for structurally similar carotenoids?
Ans:Yes, Viewer can submit the data of carotenoid either in the form of “DRAW” method or “SMILES” and the search will show the entire possible similar carotenoids list. Kindly go to the url “http://bioinfo.imtech.res.in/servers/procardb/?c=home&m=structure” and use the similar carotenoid tool.
Q: Can I verify whether my gene of interest may encode enzyme involved in carotenoid biosynthesis?
Q: What is the source of authentication of information on ProCarDB?
Ans:All the data has been compiled after extensive search in Pubmed, Google Scholar etc and all the data has relevant citation given at the bottom of each carotenoid page.
Q: How do I cite ProCarDB?
Ans:Cite as URL “http://bioinfo.imtech.res.in/servers/procardb”. As soon as the manuscript describing ProCarDB will be published, the appropriate citation information will be updated.
Q: Does ProCarDB predict genes encoding for enzymes involved in biosynthesis of carotenoids?
Ans:Yes, 30% of the given genes are predicted on the basis of literature and is highlighted with the “RED” color in the cartoon depicting the relevant pathway.
Q: How to use tools available in the database?
Ans: Structural search
This tool will be useful for the user interested in searching for carotenoids of similar or identical structure(s). Here, the users have the option of drawing a chemical query or using a smile format for the query molecule to search for carotenoids containing similar or identical structure against the query molecule. The output is displayed in a tabular format. The link to visualize the 3D structure is also available. Blast facility
We have also implemented a BLAST tool for searching similar sequences in our database. This will help the users with the local alignment of a query sequence with sequences that correspond to the genes and enzymes involved in the carotenoid biogenesis available in our database. The blast output page provides information on sequences producing significant alignments, along with e-values and scores for each of the search results. Alignment and visualization tool
The alignment and visualization tool is very important for multiple sequence alignments. This will be helpful for generating a multiple sequence alignments using ClustalW in the background. This alignment file is visualized using JalView. The JalView applet has the provision to edit, save and analyze the alignment results. HELP
The help section contains frequently asked questions (FAQs) about the database and its utility. These FAQs provide the basic information about the database, how to use the database, unique features, and interesting information about the carotenoids. The Help section also contains a tutorial about how to use the database, the type of information available to the users, and how to upload or download the information from this database.
Q: What is the meaning of the color-codes of carotenoids in the pathway?
Ans:In this database, pathways have been color-coded for ease of understanding: the pathways depicted in black indicate that the specific carotenoid has been experimentally characterized in that particular organism, and the red color in the pathway suggests that these steps are predicted based on either the presence of homologous genes or from the generalized pathway known from the literature eg. in Phaeobacterium nitratireducens, the carotenoids of spirilloxanthin series have been detected (1) hence, are black in colour while the pathway is in red color as it is predicted by us based on the pathway known from the literature in other organisms. The green color indicates that the pathway has been proposed in literature for that particular strain, eg Phaeospirillum genus (2) . The purple coloured portion of the pathway indicates that these steps of the biosynthesis pathway have been experimentally studied and validated eg. Rhodobacter sphaeroides, the entire gene cluster has been cloned and verified the function of genes and pathway was deduced.
1. Nupur, Tanuku NR, Shinichi T, Pinnaka AK: Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample. Int J Syst Evol Microbiol 2015, 65(8):2357-2364.
2. Takaichi S, Maoka T, Sasikala C, Ramana Ch V, Shimada K: Genus specific unusual carotenoids in purple bacteria, Phaeospirillum and Roseospira: structures and biosyntheses. Curr Microbiol 2011, 63(1):75-80
Q: What is the meaning of the color-codes of the genes in the pathway?
Ans:Black color-coded genes (in the pathways image) imply that such genes are present in the genome of the organism under study, purple color-coded genes denote the genes that are experimentally studied and validated, and red color-coded genes have been predicted by our group based on homology or the synthesis of downstream carotenoids.
Q: What is the brief history of carotenoids?
Ans:Carotenoid identification was initiated by Wilhelm Ferdinand Wackenroder in 1831 from the carrot which later became to known as “Carotene”. By 1902, more than 800 papers were already published. Most of the studies were performed on carotenoids extracted from plants. In 1938, Strain first used terms “Carotene” for the hydrocarbons and “xanthophylls” for oxygenated derivative of carotenes. These terms are commonly used even today. Later on Bogert (1938) suggested that xanthophylls shall be called carotenols because of their chemical structure. Russian botanist Tswett (1906, 1911) who invented chromatography, was the first person who not only separated but also purified the leaf pigments i.e. green Chls, yellow-to-orange carotenes and Xanthophylls. Later on R Wilstätter further developed methods of separation of carotenoids and was awarded Nobel Prize (1915) in chemistry. Paul Karrer recognized the symmetrical nature of the various carotenoids like beta-carotene and won Nobel Prize (1937) in chemistry. Subsequently, Richard Kühn (1935) demonstrated that alternation of single and double bonds in the carotenoids leads to absorption in the visible range and thus is responsible for pigmentation and was awarded Nobel Prize in chemistry (1938).
ProCarDB