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



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Mills, Gabrielle 



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.


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Clostridioides, Clostridium, Proteomics