## 3 Results and Discussion
### Analysis of Plasmid Presence and Antibiotic Resistance Genes
#### 3.6.3 Lanthopeptide and RiPP Gene Clusters
Protein XIJ16548, predicted by AlphaFold to be structurally similar to _Bacillus amyloliquefaciens_ subtilisism BPN (UniProt: P00782) with 35% identity and 52% positive alignment, was also linked to the _Plasmodium vivax_ SUB1 protease (PDB: 8 QKE) in HHPred and the _Plasmodium falciparum_ SUB1 protease (PDB: 8 POL) in SWISS-MODEL. Protein XIJ16549 displayed high homology to GAF domain-containing proteins, which are involved in signal transduction and ligand binding, and play key roles in regulating biological processes across various organisms (Figure S8, Table S15). BGC Region 19 Derived from _Lentzea_ sp. JNUCC 0626  
In BGC region 19, protein XIJ18177 was predicted to have functional similarity to class II lanthopeptide synthetases, such as _E. faecalis_ CylM (PDB: 5 DZT) and _B. licheniformis_ LiCM2 (PDB: 6 ST5), based on analyses from BLASTP, AlphaFold, SWISS-MODEL, and HHPred. Additionally, antiSMASH analysis identified the presence of a 41-amino acid precursor peptide (\"MSLGPIGRQYMGGDPPYSPRPPESGGLYPMCRTPARARALAG\") located downstream of the XIJ18177 protein, suggesting its role as LanM. Protein XIJ18179 was structurally predicted to resemble _P. horikoshii_ OT3 signal transduction ATPases (PDB: 6 MFV) and _E. coli_ HTH-type transcriptional regulator MaIT (PDB: 8 BOB). Further upstream, proteins XIJ18180, XIJ18181, and XIJ18183 were identified as transport-related proteins, all located in the same transcriptional orientation. Notably, typical components of Class II lanthipeptide BGCs, such as protease genes and immunity genes, were absent in this region (Figure S9, Table S16). BGC Region 21 Derived from _Lentzea_ sp. JNUCC 0626  
Biosynthetic gene cluster (BGC) region 21 contains several gene clusters involved in daptide biosynthesis. Specifically, the proteins XIJ18556 (LjvM, 248 aa), XIJ18557 (LjvD, 405 aa), XIJ18558 (LjvC, 363 aa), and XIJ18560 (LjvP, 527 aa) encode daptide-type RiPP biosynthesis enzymes: a methyltransferase, aminotransferase, dehydrogenase, and intramembrane metalloproteinases, respectively. These proteins share significant sequence similarity with their counterparts in _Microbacterium maritypicum_--MpaM (GenBank: WKT89666; 275 aa), MpaD (GenBank: WKT89671; 419 aa), MpaC (GenBank: WKT89670; 396 aa), and MpaP (GenBank: WKT89665; 562 aa)--with identity/similarity values of 37.33%/52.05%, 49.66%/63.09%, 37.32%/49.30%, and 38.15%/49.45%, respectively. Additionally, protein XIJ18549 (LjvB, 341 aa), which exhibits high homology to a daptide biosynthesis RiPP recognition protein, is homologous to two MpaB proteins from _M. maritypicum_. One MpaB (GenBank: WKT89672) consists of 349 amino acids, while the other (GenBank: WKT89673) is 335 amino acids long. The XIJ18549 protein shows 31.89% identity/43.51% similarity with the first MpaB and 34.17% identity/43.35% similarity with the second. Furthermore, three proteins in the daptide BGC--XIJ18553 (LjvK, 350 aa), XIJ18554 (LjvY, 297 aa), and XIJ18555 (LjvJ, 312 aa)--show homology to components of the _Streptomyces rochei_ lexamycin BGC (GenBank: KP823601). Specifically, they are homologous to the class V lanthionine synthetase subunit LxmK (401 aa; 36.64% identity/47.00% similarity), T3 SS effector HopA1 family protein LxmY (376 aa; 41.79% identity/51.54% similarity), and F420-dependent peptide dehydroalanine reductase LxmJ (339 aa; 48.74% identity/60.78% similarity). LxmK is responsible for catalyzing the formation of lanthionine and methylanthionine crosslinks,which are essential for the structural and functional maturation of the lanthopeptide, specifically between cysteine and dehydrated serine or threonine residues. Finally, protein XJJ18559 encodes a YcaO-like family protein. While the role of YcaO-like proteins in class V lanthopeptide biosynthesis is not fully understood, it is known that other enzymes such as LxmK, LxmJ, and LxmY are key players in this process, and YcaO-like proteins are more commonly associated with Class I-III lanthippeptides.