## 3 Results and Discussion
### Analysis of Plasmid Presence and Antibiotic Resistance Genes
#### 3.6.3 Lanthopeptide and RiPP Gene Clusters  
BGC Region 5 Derived from _Lentzea_ sp. JNUCC 0626  
An analysis of region 5 of the _Lentzea_ sp. JNUCC 0626 BCC revealed that protein XJJ15501 was predicted to have the highest structural similarity to the _Enterococcus faecalis_ class II lanthopeptide synthetase CyIM (PDB: 5 DZT) and the _Bacillus licheniformis_ LiCM2 (PDB: 6 ST5) based on HHPred and SWISS-MODEL searches. Additionally, BLASTP searches indicated that protein XJJ15502 shares similarities with various lanthionine synthetases, including LanC, LanL, and LanKC. HHPred and SWISS-MODEL analyses further suggested that protein XJJ15502 is structurally similar to the _Thermonospora curvata_ curvcidin synthetase CuvL (PDB: 8 CAR) and the _Bacillus thuringiensis_ serovar andalousiensis Class III metal-independent lanthopeptide synthetase LP-GS-ThurKC (PDB: 8 SAM). The presence of both LanM (protein XJJ15501) and a different type of lanthopeptide synthetase (protein XJJ15502) in the RiPP BGC suggests the potential for a lanthopeptide hybrid BGC involving both class II lanthopeptides and class I or III types. The antiSMASH analysis identified two precursor peptides--one with 46 amino acids and the other with 70 amino acids--located between proteins XJ15501 and XJ15502. These sequences are \"MENTIAS-CLRTGHYACSPMPLADRLSRWVPCRCSWW/SRTAVFEWW\" and \"MRTHLPEEGLAVGRT-TAAHRITGAPVSSGSRSRSRRRCRGSCPPSAARRRPSPWSAGRSRRRSSPSECTSV\", respectively. Additionally, protein XJ15500.1 contains a distinct 74-amino-acid peptide fragment. Protein XJJ15503 exhibits high homology with the GNAT family N-acetyltransferase, suggesting its potential involvement in post-translational modifications via the N-acetylation of amino acid residues in the RiPP biosynthesis pathway. This function could modulate the functional properties of RiPP peptides or alter their structures to confer new physiological activities. Moreover, protein XJ15505 shows high homology with the S9 family peptidase, indicating its potential role in the modification processes of RiPPs, such as leader sequence cleavage. For instance, protein XJ15505 could be responsible for the cleavage of the leader sequence to generate mature peptides from their precursor forms (Figure S7, Table S14). BGC Region 13 Derived from _Lentzea_ sp. JNUCC 0626  
Protein XJ16542 showed high homology to various class III LanKC proteins in BLASTP analysis, and SWISS-MODEL predicted its structure to be most similar to _T. curvata_ curvocidin synthetase CuvL (PDB: 8 CAR) and _E. faecalis_ class II lanthopeptide synthetase CyIM (PDB: 5 DZT). A potential precursor peptide, protein XJJ16543, consisting of 54 amino acids, was also identified. Proteins XJ16544 to XJ16548 exhibited similarity to radical SAM proteins, iron-containing redox enzyme family proteins, aroma-sacti cluster domain-containing proteins, AAA family ATPases, and S8 family serine peptidases, respectively. Protein XJJ16545 displayed homology to _Shewanella denitrificans_ TENA/THI-4 (PDB: 3 DDE) and methylobacterium extorquens PqqC (PDB: 5 VRC) in the HHPred analysis, and structural similarity to _Pseudomonas aeruginosa_ heme oxygenase-like oxidase (PDB: 9B9N), _Chlamydia trachomatis_ redox enzyme (PDB: 1 RCW), and _Pseudomonas protegens_ Pf-5 desaturase/decarboxylasees UndA (PDB: SV1T) was predicted by SWISS-MODEL. Protein XIJ16546 shared homology with aroma-sacti cluster domain-containing proteins, MFS transporters, and helix-turn-helix transcriptional regulators (partial) in the BLASTP analysis. Protein XIJ16547 was structurally similar to _S. coelicolor_ transcription factor AfsR (PDB: 8K60) and _Bos taurus_ adenylyl cyclase 8 (PDB: 8 BUZ) in HHPred, and to _Escherichia coli_ (PDB: 8 BOB) and _Pyrococcus horikostii_ signal transduction ATPases (PDB: 6 MFV) in SWISS-MODEL.