## 3 Results and Discussion
### Analysis of Plasmid Presence and Antibiotic Resistance Genes
#### 3.6.1. Trepene-Related Gene Clusters
Additionally, polyprenol phosphomannose-dependent alpha-1,6 mannosyltransferase MptB (XIJ18859, 482 aa) is located in the middle region of the cluster, with all genes oriented in the same transcriptional direction. The protein XIJ18858 was predicted to have structural similarity to the (2E,6E)-farnesyl diphosphate synthase from _M. tuberculosis_ (PDB: 8F8F) by AlphaFold, SWISS-MODEL, and HHPred, as well as to geranylgeranyl pyrophosphate synthases (GGPPS) from various microorganisms. GGPPS, an enzyme in the isoprenoid biosynthesis pathway, catalyzes the production of geranylgeranyl pyrophosphate (GGPP), a key precursor for terpenoid biosynthesis. It is considered a rate-limiting enzyme that influences terpene production. Photosynthetic organisms rely on GGPP to synthesize critical compounds such as carotenoids, chlorophyll side chains, and plastoquinones. GGPPS enzymes contain two conserved motifs, the first (FARM, DDX2-4D) and the second aspartate-rich motif (SARM, DDXXD). In protein XIJ18858, the motifs were present as \({}^{120}\)DDLMD\({}^{124}\) for FARM and \({}^{268}\)DDLLG\({}^{273}\) for SARM, although no large aromatic amino acids were found near the FARM motif, and the third aspartate residue of the SARM was replaced by glycine. Protein XIJ18860 showed over 90% homology to members of the squalene/phytoene synthase family, according to BLASTP analysis. This family of proteins catalyzes the head-to-head condensation of C\({}_{15}\) and C\({}_{20}\) phenyl units (e.g., famesyl diphosphate and geranylgeranyl diphosphate), key steps in steroid and carotenoid biosynthesis. Squalene synthase (SQS) catalyzes the formation of squalene from farnesyl diphosphate (FPP), while phytoene synthase (PSY) facilitates the conversion of geranylgeranyl pyrophosphate to phytoene. These two enzymes share significant structural similarities, including three highly conserved regions involved in substrate binding or catalysis. In region 23, the presence of GGPPS downstream of protein XIJ18860 suggests that the latter may function more as a PSY than as an SQS. The AlphaFold-based 3D structure prediction supported this hypothesis, revealing 59% sequence identity and 70% similarity to _S. griseus_ phytoene synthase (CrbB) in the Swiss-Prot database. A SWISS-MODEL analysis further indicated structural homology to dehydrosolane synthesases from _Enterococcus hirae_ and _Staphylococcus aureus_, reinforcing the likelihood of PSY functionality over SQS. Finally, protein XIJ18859, located within the terpene BGC of region 23, showed high amino acid sequence homology to polyprenol phosphomannose-dependent alpha-1,6 mannosyltransferase (MptB). The Swiss-Prot data indicated homology with _M. tuberculosis_ and _Corynebacterium glutamicum_ alpha-(1->6)-mannopyranosyltransferasetransferase A (MptA), with 43% and 36% sequence identity, respectively. Structural prediction tools such as SWISS-MODEL and HHPred suggested that protein XIJ18859 shared structural similarity with dolichyl pyrophosphate Man9 GlcNAc2 alpha-1,3-glucosyltransferase from _Saccharomyces cerevisiae_ (PDB: 6 SNI) and aminoarabinose transferase ArnT from _Cupiravidus metallidurans_ (PDB: 5 EZM). However, the exact function of this protein remains unclear. BGC Region 26 Derived from _Lentzea_ sp. JNUCC 0626  
The BGC in region 26 contains a single terpene cyclase gene composed of 710 amino acids (Figure S4, Table S11). Protein structure prediction using AlphaFold indicated that this gene showed the highest high-scoring segment pair (HSP) score with the germacradient/geosmin synthase from _S. coelicolor_, demonstrating 57% amino acid sequence identity and 71% similarity (positives). In comparison, the pristinol synthase from _S. pristinuespiralis_ exhibited 29% sequence identity and 46% similarity. The HHPred analysis predicted structural similarities in the C-terminal region with the selinadiene synphase from _S. pristinaespiralis_ (PDB: 4 OKZ) and in the N-terminal region with the geosmin synthase from _S. coelicolor_ (PDB: 5 DZ2).