Table 5.
Key secondary metabolite genes found in the genome of P. subalpina
| Class | Type | Gene code | SM clustera | Length (aa) | Domain structureb | Remarks |
|---|---|---|---|---|---|---|
| NRPS-like | L-alpha-aminoadipate reductase | PAC_02750 | 1167 | A-T-R | Lys2, L-lysine biosynthesis | |
| NRPS-like | adenylating reductase | PAC_02944 | 8 | 1049 | A-T-R | |
| NRPS-like | adenylating reductase | PAC_01324 | 3 | 1047 | A-T-R | |
| NRPS-like | adenylating reductase | PAC_02391 | 6 | 1023 | A-T-R | |
| NRPS-like | adenylating reductase | PAC_03877 | 10 | 1117 | A-T-R | |
| NRPS-like | adenylating reductase | PAC_04959 | 12 | 1038 | A-T-R | |
| NRPS-like | adenylating reductase | PAC_05733 | 1008 | A-T-R | ||
| NRPS-like | adenylating reductase | PAC_07003 | 1054 | A-T-R | ||
| NRPS-like | adenylating reductase | PAC_12811 | 1054 | A-T-R | ||
| NRPS-like | adenylating reductase | PAC_17490 | 1065 | A-T-R | ||
| NRPS-like | adenylating reductase | PAC_19780 | 1050 | A-T-R | ||
| NRPS-like | adenylating reductase | PAC_02202 | 5 | 1227 | A-T-R-Kinase | |
| NRPS-like | adenylating reductase | PAC_08842 | 1345 | A-T-R-KR | ||
| NRPS-like | furanone synthetase | PAC_08910 | 17 | 1013 | A-T-TE | |
| NRPS-like | quinone synthetase | PAC_14584 | 979 | A-T-TE | ||
| NRPS-like | unknown | PAC_19640 | 1394 | A-T-DUF | ||
| NRPS-like | unknown | PAC_12359 | 1655 | A-T-DUF | ||
| NRPS | PAC_05248 | 13 | 4676 | A-T-C-A-T-C-A-T-C-T-C-T-C | Siderophore biosynthesis (Ferrichrome-like) | |
| NRPS | PAC_13158 | 4838 | A-T-C-A-T-C-T-C-A-T-C-T-C-T-C | Siderophore biosynthesis (Ferrichrome-like) | ||
| NRPS | PAC_15746 | 1639 | A-T-C-T-C | |||
| NRPS | PAC_20134 | 4692 | C-A-T-C-A-T-C-A-T-C-A-T-C-T | |||
| NRPS | PAC_16560 | 565 | A-T-C | |||
| NRPS | PAC_16746 | 1207 | A-T-C | |||
| NRPS | PAC_19282 | 1220 | A-T-C | |||
| PKS-NRPS | PAC_02326 | 3974 | KS-AT-DH-MT-KR-T-C-A-T-R | |||
| PKS-NRPS | PAC_08246 | 16 | 3965 | KS-AT-DH-MT-KR-T-C-A-T-R | ||
| Type I PKS | non-reducing PKS | PAC_01338 | 4 | 2542 | SAT-KS-AT-PT-T-MT-TE | Citrinin biosynthesis-like |
| Type I PKS | non-reducing PKS | PAC_02435 | 7 | 2498 | SAT-KS-AT-PT-T-MT-TE | Citrinin biosynthesis-like |
| Type I PKS | non-reducing PKS | PAC_03302 | 2223 | KS-AT-DH-T-TE | ||
| Type I PKS | non-reducing PKS | PAC_03589 | 9 | 1670 | KS-AT-PT-T-TE | |
| Type I PKS | non-reducing PKS | PAC_07895 | 15 | 2171 | SAT-KS-AT-PT-T-T-TE | Likely melanin biosynthesis |
| Type I PKS | non-reducing PKS | PAC_08751 | 2099 | SAT-KS-AT-PT-T-T-TE | ||
| Type I PKS | non-reducing PKS | PAC_10081 | 2125 | SAT-KS-AT-PT-T-T-TE | ||
| Type I PKS | non-reducing PKS | PAC_11435 | 2169 | SAT-KS-AT-PT-T-T-TE | Likely melanin biosynthesis | |
| Type I PKS | reducing PKS | PAC_00199 | 1 | 2694 | KS-AT-DH-MT-ER-KR-T | Alternapyrone biosynthesis-like |
| Type I PKS | reducing PKS | PAC_00310 | 2 | 2283 | KS-AT-DH-ER-KR-T | |
| Type I PKS | reducing PKS | PAC_01646 | 1687 | AT-DH-MT-ER-KR-T | ||
| Type I PKS | reducing PKS | PAC_04883 | 11 | 2239 | KS-AT-DH-ER-KR-T | |
| Type I PKS | reducing PKS | PAC_06141 | 2258 | KS-AT-DH-ER-KR-T | ||
| Type I PKS | reducing PKS | PAC_10762 | 3173 | KS-AT-DH-MT-ER-KR-T-Acyltransferase | ||
| Type I PKS | reducing PKS | PAC_11350 | 3203 | KS-AT-DH-MT-ER-KR-T-Acyltransferase | ||
| Type I PKS | reducing PKS | PAC_14253 | 2590 | KS-AT-DH-MT-ER-KR-T | ||
| Type I PKS | reducing PKS | PAC_14645 | 2274 | KS-AT-DH-ER-KR-T | ||
| Type I PKS | reducing PKS | PAC_16276 | 3140 | KS-AT-DH-MT-ER-KR-T-Acyltransferase | ||
| Type I PKS | reducing PKS | PAC_17799 | 2411 | KS-AT-DH-ER-KR-T | Lovastatin-diketide synthase-like | |
| Type I PKS | reducing PKS | PAC_19082 | 2581 | KS-AT-DH-MT-ER-KR-T | ||
| Type I PKS | reducing PKS | PAC_19990 | 2970 | KS-AT-DH-MT-KR-T-C | Lovastatin-nonaketide synthase-like | |
| Type I PKS | reducing PKS | PAC_10712 | 1430 | KS-AT-TH-KR-T | 6-Methylsalicylate synthase-like PKS | |
| Type III PKS | PAC_02116 | 479 | IPR012328/IPR001099 | |||
| DMATS | PAC_15749 | 538 | IPR017795 | |||
| Terpene | PAC_05884 | 483 | ||||
| Terpene | PAC_13844 | 593 | IPR017825/IPR017825/IPR002060 | Squalene synthase-like | ||
| Terpene | PAC_15298 | 557 | ||||
| Terpene | PAC_01018 | 338 | IPR008949 | |||
| Terpene | PAC_04028 | 331 | IPR008949 | |||
| Terpene | PAC_11164 | 466 | IPR008949 | |||
| Terpene | PAC_12198 | 392 | IPR008949 | |||
| Terpene | PAC_16221 | 336 | IPR008949 |
a for details on the putative SM gene clusters see Additional file 3
b Abbreviations for domains: A adenylation, AT acyltransferase, C condensation, DH dehydratase, DUF terminal NRPS domain of unknown function, ER enoyl reductase, KR ketoreductase, KS ketosynthase, MT methyltransferase, PT product template, R reduction, SAT starter unit-ACP-transacylase, T thiolation (=acyl- or aryl- or peptidylcarrier protein), TE thioesterase, TH thiohydrolase