Final Putative Homologues of Spore Coat/Exosporium Proteins in Clostridia (GCM Thesis; Appendix 7.3)

<<used for a link in GCM Thesis>>

Appendix 7.3

PDF file containing a list of final putative homologues in Clostridia species of established spore coat and exosporium proteins from literature. The listed data includes the protein name, bacterial species, accession number of that protein in that species, and the Markov Cluster number for that protein. Markov clustering was used to validate; edges were determined using reverse BLASTp protocol with SCPS edge-weight conversion:

Refer to Appendix 7.1 and 7.2 for the first- and second- pass protocols. To verify the BLASTp homology search results, all putative proteins were analysed using MCL clustering with SCPS (spectral clustering of protein sequences) edge weight conversion of e-values. In addition to the raw homologue data, Clostridia coat proteins on UniProt (not identified in this analysis) were also included in the clustering dataset; this was done to verify their supposed identities. The inflation value was set at the recommended value of 0.2, and the edge-weight threshold was maximized. Edges were considered undirected so that only positive weights would be calculated. The clusterMaker2 application in the Cytoscape software was used to create the networks; the weak edge weight pruning threshold, number of iterations, maximum residual value, and maximum number of threads were set to their previously established values of 1E(−15), 16, 0.001, and 0—respectively. The MCL e-value threshold was set to 1E(−10) to minimize the number of proteins in each cluster. The resulting Q-value served as verification of the methodology. The overall Q value was 0.952.

Refer to Appendix 7..4 for analysis of verified homologues.

附录7.3
包含来自文献中已建立芽孢外壳和外孢子蛋白的Clostridia物种潜在同源蛋白列表的PDF文件。所列数据包括蛋白质名称、细菌物种、该物种中该蛋白质的访问号以及该蛋白质的马尔可夫聚类号。马尔可夫聚类被用于验证；边通过反向BLASTp协议与SCPS边权重转换来确定：

参照附录7.1和7.2了解第一和第二次通过协议。为了验证BLASTp同源性搜索结果，所有潜在蛋白质均使用带有SCPS（蛋白质序列的谱聚类）边权重转换的e值进行了MCL聚类分析；此外，为了验证未在此次分析中识别的Clostridia外壳蛋白在UniProt中的身份，这些蛋白也被纳入聚类数据集中；这样做是为了验证其假设的身份。膨胀值设置为推荐的0.2，边权重阈值最大化。边被视为无向的，以确保只计算正值。使用Cytoscape软件中的clusterMaker2应用程序创建网络；弱边权重修剪阈值、迭代次数、最大残差值和最大线程数分别设置为之前建立的1E(-15)、16、0.001和0。MCL e值阈值设置为1E(-10)以最小化每个聚类中的蛋白质数量。所得Q值作为方法验证的依据。整体Q值为0.952。

参照附录7..4了解验证同源蛋白的分析。