## 3 Results and Discussion
### Analysis of Plasmid Presence and Antibiotic Resistance Genes
#### 3.6.1. Trepene-Related Gene Clusters  
BGC Region 1 Derived from _Lentzea_ sp. JNUCC 0626  
The BLASTP analysis of region 1 in the BGCs of _Lentzea_ sp. JNUCC 0626 revealed that both copies of Family 2 encapsulin nanocompartment cargo protein terpene cyclases (EncT, proteins XIJ14781 and XIJ14782) and Family 2B encapsulin nanocompartment shell proteins (EncS, proteins XIJ14780 and XIJ14783; referred to as Esh in this study) are arranged in the same transcriptional orientation. Downstream of this region, other proteins such as XIJ14779 (a distinct terpene cyclase/polyprenryl transferase), XIJ14778 (4-hydroxy-3-methylbut-2-enyl diphosphate reductase), and XIJ14777 (1-Deoxy-D-xylulose-5-phosphate synthase) are organized in an operon-like structure (Figure 3, Table S7). AlphaFold predicted that protein XIJ14779 shares a tertiary structure with (2E,6E)-farnesyl diphosphate synthases from _Mycobacterium tuberculosis_ (UniProt: P9 WKH1) and _Mycobacterium bovis_ (UniProt: P0A5H9), with a sequence identity of 48% and 61% similarity. HHPed structural analysis further suggested that protein XIJ14779.1 resembles sesquiterpene cyclases, such as _Kitasatospora setae hedycaryl_ synthase (PDB: 4 MC3), _Streptomyces peristinaespiralis_ seli-nadiene synthase (PDB: 4 OKZ), and _Streptomyces coelicolor_ epi-isozizaene synthase (PDB: 8 SU3), as well as the monoterepne cyclase _S. coelicolor_ geosmin synthase (PDB: 5 DZ2). The SWISS-MODEL analysis indicated a broader structural similarity with bacterial terpene cyclases, such as _S. coelicolor_ polyprenryl synthetase (PDB: 3 NF2), _Pyrococcus horikoshi_ geranyl pyrophosphate synthetase (PDB: 1 WY0), and _Rladobacter capsulatus_ decaprenryl diphosphate synthase (PDB: 3 MZV). Protein XIJ14779 contains the conserved motifs of trans-prenyltransferases, including the \"first aspartate-rich motif\" (FARM, DDX-4D) and the \"second aspartate-rich motif\" (SARM, DDXD), with motifs \({}^{104}\)DDVMD\({}^{107}\) (FARM) and \({}^{234}\)DDXXD\({}^{238}\) (SARM). Notably, the third aspartate in the SARM motif is replaced by glycine at position 238. Proteins XIJ14781 (337 aa) and XIJ14782 (359 aa) were annotated as EncT based on the BLASTP analysis. The structural predictions made by AlphaFold, HHPed, and SWISS-MODEL revealed similarities to germacradientol/geosmin synthase, pentalenene synthase, and epi-isozizaene synthase. However, the sequence identity between proteins XIJ14781 and XIJ14782 was only 36.18%, with a similarity of 51.68%, which is relatively low. Moreover, neither protein exhibited the conserved FARM and SARM motifs typically found in GGDPS and other prenyltransferases. These terpene cyclases are specialized enzymes operating within encapsulin nanocompartments, enhancing their efficiency. Proteins XIJ14780 (466 aa) and XIJ14783 (468 aa) were both annotated as cyclic nucleotide-binding domain-containing proteins, EncS proteins, and Crp/Fnr family transcriptional regulators in the BLASTP analysis. Compared to the proteins XIJ14779 and XIJ14782, XIJ14780 and XIJ14783 showed a high sequence identity (62.24%) and similarity (77.85%). No structural homologs were found for protein XIJ14780 in AlphaFold and SwissProt, but TrEMBL predicted a structure resembling those from _Lentzea_ sp. The HHPed analysis showed that the N-terminus of protein XIJ14780 shared structural homology with cyclic AMP-dependent transcriptional regulators from _Corynebacterium glutamicum_, _Agathobacter retalis_, and _Thermus thermophilus_, while the C-terminus resembled the encapsulin shell of the _Acinetobacter baumanni_ family 2A cargo-loaded encapsulin. In contrast, protein XIJ14783 showed structural homology to eukaryotic cGMP-dependent protein kinase regulatory subunits, such as those from _Homo sapiens_, _Euglena gracilis_, _Mus musculus_, _Bos taurus_, _Trypanosoma cruzi_, and _Rattus norvegicus_, as revealed by SWISS-MODEL.