4.1. In silico identification of LysinB_MF and characterization

Lysin B from D29 (GenBank: {"type":"entrez-protein","attrs":{"text":"AAC18452.1","term_id":"3172259","term_text":"AAC18452.1"}}AAC18452.1) was blasted (^{Altschul et al., 1990}) against all the genomes available in the NCBI database for M. fortuitum (tax id: 1766), possibly harbouring prophages. The M. fortuitum genome with the top lysin hits (LysinB_MF) was subjected to PHAST (^{Zhou et al., 2011}) and to annotate and fix frameshifts in these genomes, the RAST server was used. The CGview tool (^{Grant & Stothard, 2008}) was used to build the genome map of the first hit, phiE1336. Cluster-wise sequences of LysinB were downloaded from the Actinobacteriophage Database (https://phagesdb.org/), and domains of those lysins were predicted using InterProScan 5 (^{Quevillon et al., 2005}). ClustalW (^{Thompson et al., 1994}) and ESPript (https://espript.ibcp.fr) (^{Robert & Gouet, 2014}) were used to generate alignment files which were then used to create phylogenetic trees using Interactive Tree Of Life (iTOL) v5 (^{Letunic & Bork, 2021}). The tertiary structure of LysinB_MF was downloaded from the AlphaFold Protein Structure Database (^{Varadi et al., 2023}) and visualized using PyMOL (https://pymol.org/2/). The POLYVIEW-MM tool was used to predict conserved residues in the tertiary structure of LysinB_MF (^{Porollo & Meller, 2010}). The DALI server was used to find structures similar to the LysinB_MF (^{Holm, 2022}) and eF-surf was used to predict the electrostatic potential of the enzyme (^{Nielsen et al., 1999}). Conservation analysis was done by analyzing the Pfam entry of PGBD (PF01471) against all the proteins available in the UniProt database (https://www.uniprot.org/). TaxIDs were used to detect the presence of this domain across several species using the InterPro classification of protein family website (https://www.ebi.ac.uk/interpro/).