diff --git a/docs/glossary.md b/docs/glossary.md
index 9033ef4..75017c0 100644
--- a/docs/glossary.md
+++ b/docs/glossary.md
@@ -18,19 +18,25 @@ The types of cluster within each ruleset are given below:
|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|
+|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|5.0|
+|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|
@@ -39,11 +45,11 @@ The types of cluster within each ruleset are given below:
|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|
-|LAP|Linear azol(in)e-containing peptides|<= 3.0|6.0|
|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|
@@ -52,15 +58,17 @@ The types of cluster within each ruleset are given below:
|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-like|Molecules containing mycosporine-like amino acid|7.0|7.0|
+|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|7.1|
-|NRPS|Non-ribosomal peptide synthetase|<= 3.0|6.0|
+|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|
@@ -70,6 +78,8 @@ The types of cluster within each ruleset are given below:
|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 |
@@ -80,17 +90,15 @@ The types of cluster within each ruleset are given below:
|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|
-|saccharide|Saccharide (loose strictness, likely from primary metabolism)|<= 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|4.1|
+|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|
-|thiopeptide|Thiopeptide|4.2|5.0|
-|transAT-PKS|Trans-AT PKS|<= 3.0|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|
@@ -98,11 +106,12 @@ The types of cluster within each ruleset are given below:
|Label|Description|Added|Last updated|
|-----|-----------|:---:|:----------:|
|fungal-RiPP-like|Fungal RiPP-likes|7.0|7.0|
-|NRPS-like|NRPS-like fragment|5.0|5.0|
+|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
@@ -110,12 +119,17 @@ The types of cluster within each ruleset are given below:
|-----|-----------|:---:|:----------:|
|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*|