Cellobiose dehydrogenase sequences analysis

Sequence alignments from different cellobiose dehydrogenase classes, coming from database mining and sequence similarity network analysis, as described in the published article: Giorgianni, A.; Zenone, A.; Sützl, L.; Csarman, F.; Ludwig, R. Exploring Class III Cellobiose Dehydrogenase: Sequence Analysis and Optimized Recombinant Expression. Microb. Cell Fact. 2024, 23, 146, doi: 10.1186/s12934-024-02420-2. The dataset includes sequence alignments after the separation into different classes (e.g. Class_I.fasta), after the removal of all the sequences lacking a signal peptide (e.g. Class_I_noSP.fasta), and the removal of 99% redundancy (e.g. Class_I_noSP_red99.fasta). To remove sequences lacking the signal peptide we used Signal P 5.0 (https://services.healthtech.dtu.dk/services/SignalP-5.0/) [Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37(4):420–3]. Also included is the alignment of sequences trimmed and used for phylogenetic tree analysis as described in the published article. The alignments were obtained using MAFFT (G-INS-I algorithm) [Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80].