Version 1 features#
Version 1.0 of plantiSMASH is live now!
plantiSMASH is an extension of antiSMASH optimized for plant genomes. Version 1 includes:
- Specific library of pHMM models and new cluster calling logic
- Plant-specific ClusterBlast database
- GlimmerHMM-based gene prediction
- Homology-based metabolic modeling
- Coexpression analysis and HTML-based visualization with the CoExpress module
Supported Cluster Types (version 1)#
| Rule | Min. Generic Domains* | Special Domains Required |
|---|---|---|
| alkaloid | 3 | Bet_v_1, Cu_amine_oxid, Str_synth |
| cyclopeptide | — | BURP |
| fatty_acid | — | — (not defined in v1) |
| lignan | 3 | Dirigent |
| phenolamide | — | — (not defined in v1) |
| plant | 4 | None |
| polyketide | 3 | Chal_sti_synt_C, Chal_sti_synt_N |
| saccharide | 3 | Glycos_transf_1, Glycos_transf_2, Glycos_transf_28, UDPGT, UDPGT_2 |
| sesterterpene | 2 | Terpene_synth_C, polyprenyl_synt |
| strictosidine_like | — | — (not defined in v1) |
| terpene | 3 | Terpene_synth, Terpene_synth_C, Prenyltrans, SQHop_cyclase_C, SQHop_cyclase_N, PRISE |
| transporter | — | — (not defined in v1) |
* Generic domains in version 1:
cMT, nMT, oMT, adh_short, Chal_sti_synt_C, Chal_sti_synt_N, COesterase, UDPGT, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, Lycopene_cycl, NAD_binding_1, p450, SQHop_cyclase_C, SQHop_cyclase_N, Prenyltrans, Terpene_synth_C, Terpene_synth, Transferase, Aminotran_1_2, AMP-binding, DIOX_N, Dirigent, Bet_v_1, Cu_amine_oxid, Str_synth, Trp_syntA, His_biosynth, adh_short_C2, Peptidase_S10, Prenyltransf, Epimerase, 2OG-FeII_Oxy, Aminotran_3, Methyltransf_2, Methyltransf_3, Methyltransf_7, PRISE, Cellulose_synt, Chalcone, ERG4_ERG24, FA_desaturase, FA_desaturase_2, Methyltransf_11, polyprenyl_synt, SE, SQS_PSY, TPMT, UbiA, Lipoxygenase, Lyase_aromatic, HMGL-like, Chalcone_3, Chalcone_2, Acetyltransf_1, UDPGT_2, GMC_oxred_N, GMC_oxred_C, Amino_oxidase, DAHP_synth_1, DAHP_synth_2
plantiSMASH GitHub