Protocluster Types#
antiSMASH uses some abbreviations internally and in outputs to refer to the different types of secondary metabolite clusters detected.
There are three strictness levels for cluster detection: strict, relaxed, and loose. Each level includes the more strict levels. The types of cluster within each ruleset are given below:
Current Types#
Strict#
| Label | Description | Added | Last updated |
|---|---|---|---|
| 2dos | 2-deoxy-streptamine aminoglycoside | 7.0 | 7.0 |
| acyl_amino_acids | N-acyl amino acid | 4.0 | 4.1 |
| amglyccycl | Aminoglycoside/aminocyclitol | <= 3.0 | <= 3.0 |
| aminocoumarin | Aminocoumarin | <= 3.0 | <= 3.0 |
| aminopolycarboxylic-acid | Aminopolycarboxylic acid metallophores (doi:10.1039/C8MT00009C) | 7.0 | 7.0 |
| archaeal-RiPP | Archaeal RiPPs (doi:10.1021/jacs.2c00521 supplemental) | 7.1 | 7.1 |
| arylpolyene | Aryl polyene | <= 3.0 | <= 3.0 |
| atropopeptide | Atropopeptide RiPPs, e.g. scabrirubin and tryptorubin | 8.0 beta | 8.0 beta |
| azoxy-crosslink | axoxy compounds formed by carboxilic cross-link | 8.0 beta | 8.0 beta |
| azoxy-dimer | axoxy compounds formed by dimerisation | 8.0 beta | 8.0 beta |
| betalactone | Beta-lactone containing protease inhibitor | 5.0 | 5.0 |
| blactam | β-lactam | <= 3.0 | <= 3.0 |
| bottromycin | Bottromycin | <= 3.0 | <= 3.0 |
| butyrolactone | Butyrolactone | <= 3.0 | <= 3.0 |
| CDPS | tRNA-dependent cyclodipeptide synthases | 5.0 | 8.0 beta |
| crocagin | Crocagin-like | 7.0 | 7.0 |
| cyanobactin | Cyanobactins like patellamide (AY986476) | <= 3.0 | 7.0 |
| cyclic-lactone-autoinducer | agrD-like cyclic lactone autoinducer peptides (AF001782) | 6.0 | 6.0 |
| cytokinin | Adenine-type cytokinins, e.g. fusatin and trans-zeatin | 8.0 beta | 8.0 beta |
| darobactin | Darobactin-like compounds | 7.1 | 7.1 |
| deazapurine | Deazapurine | 8.0 beta | 8.0 beta |
| ectoine | Ectoine | <= 3.0 | <= 3.0 |
| epipeptide | D-amino-acid containing RiPPs such as yydF (D78193) | 6.0 | 6.0 |
| fungal_CDPS | Fungal cyclodipeptide synthases | 8.0 beta | 8.0 beta |
| fungal-RiPP | Fungal RiPP with POP or UstH peptidase types and a modification | 5.0 | 5.0 |
| furan | Furan | <= 3.0 | 5.0 |
| glycocin | Glycocin | <= 3.0 | <= 3.0 |
| guanidinotides | Pheganomycin-style protein ligase-containing cluster | 4.0 | 6.0 |
| hglE-KS | Heterocyst glycolipid synthase-like PKS | 5.0 | 5.0 |
| HR-T2PKS | Highly reducing type II PKS like ishigamide and skyllamycin | 7.1 | 7.1 |
| hserlactone | Homoserine lactone | <= 3.0 | <= 3.0 |
| hydrogen-cyanide | Hydrogen cyanide (AF208523, doi:10.1128/jb.182.24.6940-6949.20) | 7.1 | 7.1 |
| hydroxy-tropolone | 7-hydroxytropolone-like cluster | 8.0 beta | 8.0 beta |
| HR-T2PKS | Highly reducing type II PKS like ishigamide and skyllamycin | 7.1 | 7.1 |
| indole | Indole | <= 3.0 | 4.0 |
| isocyanide | Isocyanides (doi:10.1093/nar/gkad573) | 7.1 | 7.1 |
| NRP with isocyanide | Isocyanides (doi:0.1128/mBio.00785-18) | 7.1 | 7.1 |
| ladderane | Ladderane | <= 3.0 | 7.1 |
| lanthipeptide class I | Class I lanthipeptides like nisin | 4.2 | 6.0 |
| lanthipeptide class II | Class II lanthipeptides like mutacin II (U40620) | 4.2 | 6.0 |
| lanthipeptide class III | Class III lanthipeptides like labyrinthopeptin (FN178622) | 4.2 | 6.0 |
| lanthipeptide class IV | Class IV lanthipeptides like venezuelin (HQ328852) | 4.2 | 6.0 |
| lanthipeptide class V | Glycosylated lanthipeptide/linaridin hybrids like MT210103 | 5.1 | 6.0 |
| lassopeptide | Lasso peptide | <= 3.0 | 5.0 |
| linaridin | Linear arid peptide such as cypemycin (HQ148718) and salinipeptin (MG788286) | <= 3.0 | <= 3.0 |
| lincosamides | NRPS-adjacent biosynthesis of lincosamides | 8.0 beta | 8.0 beta |
| lipolanthine | Lanthipeptide class containing N-terminal fatty acids such as MG673929 | 5.0 | 5.0 |
| melanin | Melanin | <= 3.0 | <= 3.0 |
| methanobactin | Copper-chelating/transporting peptides (doi:10.1126/science.aap9437) | 7.0 | 7.0 |
| microviridin | Microviridin | <= 3.0 | <= 3.0 |
| mycosporine | Molecules containing mycosporine-like amino acid | 7.0 | 8.0 beta |
| NAGGN | N-acetylglutaminylglutamine amide | 5.0 | 5.0 |
| NAPAA | Non-alpha poly-amino acids like e-Polylysin | 6.0 | 7.0 |
| NI-siderophore | NRPS-independent, IucA/IucC-like siderophores (siderophore prior to 7.0) | 7.0 | 8.0 beta |
| nitropropanoic-acid | 3-Nitropropanoic acid (neurotoxin) | 8.0 beta | 8.0 beta |
| NRPS | Non-ribosomal peptide synthetase | <= 3.0 | 8.0 beta |
| NRP-metallophore | Non-ribosomal peptide metallophores | 7.0 | 7.0 |
| nucleoside | Nucleoside | <= 3.0 | 5.0 |
| oligosaccharide | Oligosaccharide | <= 3.0 | <= 3.0 |
| opine-like-metallophore | Opine-like zincophores like staphylopine (doi:10.1128/mSystems.00554-20) | 7.0 | 7.0 |
| other | Cluster containing a secondary metabolite-related protein that does not fit into any other category | 4.0 | 5.0 |
| PBDE | Polybrominated diphenyl ether | 4.1 | 4.1 |
| phenazine | Phenazine | <= 3.0 | <= 3.0 |
| phosphoglycolipid | Phosphoglycolipid | <= 3.0 | <= 3.0 |
| phosphonate | Phosphonate | <= 3.0 | 7.0 |
| polyhalogenated-pyrrole | Polyhalogenated pyrrole | 8.0 beta | 8.0 beta |
| polyyne | Polyyne | 8.0 beta | 8.0 beta |
| PpyS-KS | PPY-like pyrone | 4.2 | 4.2 |
| prodigiosin | Serratia-type non-traditional PKS prodigiosin biosynthesis pathway | 6.0 | 6.0 |
| proteusin | Proteusin | <= 3.0 | <= 3.0 |
| PUFA | Polyunsaturated fatty acid | <= 3.0 | <= 3.0 |
| pyrrolidine | Pyrrolidines like described in BGC0001510 | 6.0 | 6.0 |
| ranthipeptide | Cys-rich peptides (aka. SCIFF: six Cys in fourty-five) like in CP001581:3481278-3502939 | 6.0 | 6.0 |
| RaS-RiPP | Streptide-like thioether-bond RiPPs | 5.0 | 5.0 |
| RCDPS | Fungal Arginine-containing cyclic dipeptides | 7.0 | 7.0 |
| redox-cofactor | Redox-cofactors such as PQQ (NC_021985:1458906-1494876) | 6.0 | 6.0 |
| resorcinol | Resorcinol | <= 3.0 | <= 3.0 |
| sactipeptide | Sactipeptide | <= 3.0 | 6.0 |
| spliceotide | RiPPs containing plpX type spliceases (NZ_KB235920:17899-42115) | 6.0 | 6.0 |
| T1PKS | Type I PKS (Polyketide synthase) | <= 3.0 | <= 3.0 |
| T2PKS | Type II PKS | <= 3.0 | 5.0 |
| T3PKS | Type III PKS | <= 3.0 | <= 3.0 |
| terpene | Terpene | <= 3.0 | 8.0 beta |
| thioamitides | Thioamitide RiPPs as found in JOBF01000011 | 5.1 | 6.0 |
| thioamide-NRP | Thioamide-containing non-ribosomal peptide | 5.0 | 5.0 |
| transAT-PKS | Trans-AT PKS | <= 3.0 | 8.0 beta |
| triceptide | Triceptides | 7.1 | 7.1 |
| tropodithietic-acid | Tropodithietic acid | 5.0 | 5.0 |
Relaxed#
| Label | Description | Added | Last updated |
|---|---|---|---|
| fungal-RiPP-like | Fungal RiPP-likes | 7.0 | 7.0 |
| NRPS-like | NRPS-like fragment | 5.0 | 8.0 beta |
| phosphonate-like | Phosphonate-like (prior to 7.0 this was the phosphonate rule) | 7.0 | 7.0 |
| PKS-like | Other types of PKS | 5.0 | 5.0 |
| RiPP-like | Other unspecified ribosomally synthesised and post-translationally modified peptide product (RiPP) | 4.1 | 7.0 |
| RRE-containing | RRE-element containing cluster | 6.0 | 6.0 |
| terpene-precursor | Compound likely used as a terpene precursor | 8.0 beta | 8.0 beta |
| transAT-PKS-like | Trans-AT PKS fragment, with trans-AT domain not found | <= 5.0 | 5.0 |
Loose#
| Label | Description | Added | Last updated |
|---|---|---|---|
| fatty_acid | Fatty acid (loose strictness, likely from primary metabolism) | <= 3.0 | 4.2 |
| halogenated | Halogenase-containing cluster, potentially generating a halogenated product | 5.0 | 5.0 |
| lysine | Fungal lysine primary metabolism | 8.0 beta | 8.0 beta |
| saccharide | Saccharide (loose strictness, likely from primary metabolism) | <= 3.0 | <= 3.0 |
Obsolete/Previous Types#
| Label | Description | Added | Removed | Notes |
|---|---|---|---|---|
| LAP | Linear azol(in)e-containing peptides | <= 3.0 | 8.0 beta | Merged with thiopeptide into azole-containing RiPP |
| mycosporine-like | Molecules containing mycosporine-like amino acid | 7.0 | 8.0 beta | Renamed to mycosporine |
| thiopeptide | Thiopeptide | 4.2 | 8.0 beta | Merged with LAP into azole-containing RiPP |
| siderophore | Siderophore | <= 3.0 | 7.0 | Renamed to NI-siderophore |
| bacteriocin | Bacteriocin or other unspecified ribosomally synthesised and post-translationally modified peptide product (RiPP) |
4.1 | 6.0 | Renamed to RiPP-like |
| fused | Pheganomycin-style protein ligase-containing cluster | 4.0 | 6.0 | Renamed to guanidinotides |
| head_to_tail | Head-to-tail cyclised RiPP (subtilosin-like) | <= 3.0 | 6.0 | Merged into sactipeptides |
| lanthidin | Glycosylated lanthipeptide/linaridin hybrids like MT210103 | 5.1 | 6.0 | Renamed to lanthipeptide class V |
| lanthipeptide | Lanthipeptides | 4.2 | 6.0 | Split into subclasses, e.g. lanthipeptide class I |
| TfuA-related RiPPs | 5.1 | 6.0 | Renamed to thioamitides | |
| otherks | Other types of PKS | <= 3.0 | 5.0 | Split into PKS-like and hglE-KS |
| microcin | Microcin | <= 3.0 | 5.0 | Merged into lasso peptide |
| cf_saccharide | Possible saccharide | <= 3.0 | 5.0 | Renamed to saccharide |
| cf_fatty_acid | Possible fatty acid | <= 3.0 | 5.0 | Renamed to fatty_acid |
| cf_putative | Putative cluster of unknown type identified with the ClusterFinder algorithm |
<= 3.0 | 5.0 | These predictions are now subregions, not clusters |