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].本数据集包含不同类别的纤维二糖脱氢酶（cellobiose dehydrogenase）的序列比对结果，相关数据通过数据库挖掘与序列相似性网络分析获取，其配套研究已发表于论文：Giorgianni, A.; Zenone, A.; Sützl, L.; Csarman, F.; Ludwig, R. 探索III类纤维二糖脱氢酶：序列分析与优化重组表达. 《微生物细胞工厂》（Microb. Cell Fact.）2024, 23, 146, doi: 10.1186/s12934-024-02420-2. 本数据集涵盖三类序列比对文件：经分类后的原始序列比对文件（例如Class_I.fasta）、剔除所有缺失信号肽序列后的比对文件（例如Class_I_noSP.fasta），以及移除99%冗余序列后的比对文件（例如Class_I_noSP_red99.fasta）。本次研究使用SignalP 5.0工具（https://services.healthtech.dtu.dk/services/SignalP-5.0/）[Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S等. 基于深度神经网络的SignalP 5.0可优化信号肽预测. 《自然-生物技术》（Nat Biotechnol.）2019;37(4):420–3.] 完成缺失信号肽序列的筛选剔除。 此外，本数据集还包含经修剪后用于系统发育树分析的序列比对结果，相关细节已刊载于前述研究论文。本次序列比对采用MAFFT（G-INS-I算法）工具完成[Katoh K, Standley DM. MAFFT多序列比对软件7版：性能与易用性优化. 《分子生物学与进化》（Mol Biol Evol.）2013;30(4):772–80.]。