UPObase

UPObase curates fungal unspecific peroxygenase (UPO) and UPO-like enzyme sequences and provides classification and sequence-analysis resources to support studies of enzyme function and evolution.

Key Features:

• Extensive Sequence Repository: Houses 1948 peroxygenase-encoding protein sequences derived from over 800 fungal genomes.
• Genome mining from Ensembl: Operates as part of a genome-mining pipeline that compiles sequences from the fungal kingdom by leveraging data in the Ensembl database.
• Advanced Search Capabilities: Supports systematic searches by organism name, cluster ID, and accession number.
• Classification and Annotation Tools: Classifies UPOs into subfamilies I–V and an undetermined Pog group, including six Pog sub-superfamilies (Pog-a–Pog-f) and intra-subfamily groups Ia/Ib and IIIa/IIIb, with signature motifs used for annotation.
• Sequence Analysis Functions: Provides multiple sequence alignments and phylogenetic tree construction for evolutionary and comparative analyses.

Scientific Applications:

• Enzyme engineering: Supports engineering of unspecific peroxygenases by providing classified sequence diversity and motif information.
• Functional annotation and classification: Facilitates annotation and classification of UPOs and UPO-like enzymes across fungal genomes.
• Evolutionary and phylogenetic studies: Enables phylogenetic analysis of UPO families and inference of evolutionary relationships using alignments and trees.
• Biocatalysis and biotechnology exploration: Aids exploration of UPO catalytic activities, including epoxidation, peroxygenation, and electron oxidations, for biocatalysis applications.
• Fungal metabolism research: Supports studies of fungal metabolism by cataloging secreted peroxygenases across fungal species.

Methodology:

Sequence compilation via a genome-mining pipeline using Ensembl data; classification based on signature motifs; analyses performed using multiple sequence alignments and phylogenetic tree construction.