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 8.0
azole-containing-RiPP (Thio)azol(in)e-containing peptides, linear and macrocyclic 8.0 8.0
azoxy-crosslink Axoxy compounds formed by carboxilic cross-link 8.0 8.0
azoxy-dimer Axoxy compounds formed by dimerisation 8.0 8.0
benzoxazole Benzoxazoles 8.0 8.0
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
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 8.0
darobactin Darobactin-like compounds 7.1 7.1
deazapurine Deazapurine 8.0 8.0
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 8.0
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 8.0
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 8.0
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
leupeptin Leupeptin-like compounds 8.0 8.0
linaridin Linear arid peptide such as cypemycin (HQ148718) and salinipeptin (MG788286) <= 3.0 <= 3.0
lincosamides NRPS-adjacent biosynthesis of lincosamides 8.0 8.0
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
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
nitropropanoic-acid 3-Nitropropanoic acid (neurotoxin) 8.0 8.0
NRPS Non-ribosomal peptide synthetase <= 3.0 8.0
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 8.0
polyyne Polyyne 8.0 8.0
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
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
triceptide Triceptides 7.1 7.1
tropodithietic-acid Tropodithietic acid 5.0 5.0

Relaxed#

Label Description Added Last updated
NRPS-like NRPS-like fragment 5.0 8.0
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 8.0
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
fungal-RiPP-like Fungal RiPP-likes 7.0 8.0
halogenated Halogenase-containing cluster, potentially generating a halogenated product 5.0 5.0
lysine Fungal lysine primary metabolism 8.0 8.0
quinone_isoprenoid_chain Quinone isoprenoid side chain prenyltransferase (e.g. coenzyme Q, menaquinone) 8.0 8.0
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 Merged with thiopeptide into azole-containing RiPP
mycosporine-like Molecules containing mycosporine-like amino acid 7.0 8.0 Renamed to mycosporine
thiopeptide Thiopeptide 4.2 8.0 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 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