Laccases and other oxidoreductases are good
negative sets, since these enzymes and peroxidases share the same nature in transferring electrons from one to another but take different electron donors and acceptors. As a result, all 77 protein sequences belonging to eight peroxidase families were correctly predicted by the corresponding sequence profiles in our pipeline. Furthermore, none of the 236 protein sequences from the negative set showed any significant hits. In fact, many sequences in the negative set showed insignificant hits which had far higher E-values than the identification threshold 1.0e-5. These results clearly supported the NVP-BGJ398 nmr quality of the pipeline in the accuracy and discrimination power against the positive and negative sets, respectively. System architecture fPoxDB is built on a three-tiered system which consists of database, application, and user interface tiers. The database tier embraces database servers which run on MySQL relational database management system. The application tier is comprised of system monitoring servers and computing nodes which coordinates and schedules BLAST [41], HMMER [31], BLASTMatrix [32], ClustalW [42], and analysis jobs submitted from the website. The user interface tier adopts data-driven
user interface (DUI), originally designed for the CFGP 2.0 [32], which runs on the Apache HTTP Server. Servers for each tier are physically separated
to balance load, providing Cisplatin ic50 comfortable user experience of fPoxDB. In-house scripts for the identification pipeline were written in Perl. The web interface follows HTML5 and CSS3 standard to support cross-browsing. Example of the database Sinomenine usage Investigation of gene duplication and loss could help us to understand how fungi adapt to different environments. Catalases are haem peroxidases in which structure is well conserved throughout all domains of life [37]. They have been phylogenetically studied in both prokaryotes and eukaryotes [37, 43], however, not in detail for fungi. To demonstrate how fPoxDB could be used in comparative and evolutionary studies, amino acid sequences of a domain commonly found in 109 catalases from 32 species were analysed. To elucidate evolutionary history of catalases, a reconciliation analysis was conducted. The reconciled tree revealed that duplication or loss events of catalase genes occurred https://www.selleckchem.com/products/lazertinib-yh25448-gns-1480.html frequently in most of the internal and leaf nodes (Additional file 2). Except for three nodes, all internal nodes underwent multiple gene losses or duplications in fungal clades. Interestingly, only gene losses occurred in members of Ascomycota at the species-level. In contrast, gene losses as well as duplications were found to have occurred in species belonging to Basidiomycota.