glossary: update rules for 8.0 beta

docs/glossary.md

@@ -18,19 +18,25 @@ The types of cluster within each ruleset are given below:
 |<span id="amglyccycl">amglyccycl</span>|Aminoglycoside/aminocyclitol|&lt;= 3.0|&lt;= 3.0|
 |<span id="aminocoumarin">aminocoumarin</span>|Aminocoumarin|&lt;= 3.0|&lt;= 3.0|
 |<span id="aminopolycarboxylic-acid">aminopolycarboxylic-acid</span>|Aminopolycarboxylic acid metallophores (doi:10.1039/C8MT00009C)|7.0|7.0|
-|<span id="archaeal-RiPP">archaeal-RiPP</span>|Archaeal RiPPs (doi:10.1021/jacs.2c00521 supplemental)|7.1|7.1|
+|<span id="archaeal-ripp">archaeal-RiPP</span>|Archaeal RiPPs (doi:10.1021/jacs.2c00521 supplemental)|7.1|7.1|
 |<span id="arylpolyene">arylpolyene</span>|Aryl polyene|&lt;= 3.0|&lt;= 3.0|
+|<span id="atropopeptide">atropopeptide</span>|Atropopeptide RiPPs, e.g. scabrirubin and tryptorubin|8.0 beta|8.0 beta|
+|<span id="azoxy-crosslink">azoxy-crosslink</span>|axoxy compounds formed by carboxilic cross-link|8.0 beta|8.0 beta|
+|<span id="azoxy-dimer">azoxy-dimer</span>|axoxy compounds formed by dimerisation|8.0 beta|8.0 beta|
 |<span id="betalactone">betalactone</span>|Beta-lactone containing protease inhibitor|5.0|5.0|
 |<span id="blactam">blactam</span>|&beta;-lactam|&lt;= 3.0|&lt;= 3.0|
 |<span id="bottromycin">bottromycin</span>|Bottromycin|&lt;= 3.0|&lt;= 3.0|
 |<span id="butyrolactone">butyrolactone</span>|Butyrolactone|&lt;= 3.0|&lt;= 3.0|
-|<span id="cdps">CDPS</span>|tRNA-dependent cyclodipeptide synthases|5.0|5.0|
+|<span id="cdps">CDPS</span>|tRNA-dependent cyclodipeptide synthases|5.0|8.0 beta|
 |<span id="crocagin">crocagin</span>|Crocagin-like|7.0|7.0|
 |<span id="cyanobactin">cyanobactin</span>|Cyanobactins like patellamide (AY986476)|&lt;= 3.0|7.0|
 |<span id="cyclic-lactone-autoinducer">cyclic-lactone-autoinducer</span>|agrD-like cyclic lactone autoinducer peptides (AF001782)|6.0|6.0|
+|<span id="cytokinin">cytokinin</span>|Adenine-type cytokinins, e.g. fusatin and trans-zeatin|8.0 beta|8.0 beta|
 |<span id="darobactin">darobactin</span>|Darobactin-like compounds|7.1|7.1|
+|<span id="deazapurine">deazapurine</span>|Deazapurine|8.0 beta|8.0 beta|
 |<span id="ectoine">ectoine</span>|Ectoine|&lt;= 3.0|&lt;= 3.0|
 |<span id="epipeptide">epipeptide</span>|D-amino-acid containing RiPPs such as yydF (D78193)|6.0|6.0|
+|<span id="fungal_cdps">fungal_CDPS</span>|Fungal cyclodipeptide synthases|8.0 beta|8.0 beta|
 |<span id="fungal-ripp">fungal-RiPP</span>|Fungal RiPP with POP or UstH peptidase types and a modification|5.0|5.0|
 |<span id="furan">furan</span>|Furan|&lt;= 3.0|5.0|
 |<span id="glycocin">glycocin</span>|Glycocin|&lt;= 3.0|&lt;= 3.0|
@@ -39,11 +45,11 @@ The types of cluster within each ruleset are given below:
 |<span id="HR-T2PKS">HR-T2PKS</span>|Highly reducing type II PKS like ishigamide and skyllamycin|7.1|7.1|
 |<span id="hserlactone">hserlactone</span>|Homoserine lactone|&lt;= 3.0|&lt;= 3.0|
 |<span id="hydrogen-cyanide">hydrogen-cyanide</span>|Hydrogen cyanide (AF208523, doi:10.1128/jb.182.24.6940-6949.20)|7.1|7.1|
+|<span id="hydroxytropolone">hydroxy-tropolone</span>|7-hydroxytropolone-like cluster|8.0 beta|8.0 beta|
 |<span id="HR-T2PKS">HR-T2PKS</span>|Highly reducing type II PKS like ishigamide and skyllamycin|7.1|7.1|
 |<span id="indole">indole</span>|Indole|&lt;= 3.0|4.0|
 |<span id="isocyanide">isocyanide</span>|Isocyanides (doi:10.1093/nar/gkad573)|7.1|7.1|
 |<span id="isocyanide-nrp">NRP with isocyanide</span>|Isocyanides (doi:0.1128/mBio.00785-18)|7.1|7.1|
-|<span id="lap">LAP</span>|Linear azol(in)e-containing peptides|&lt;= 3.0|6.0|
 |<span id="ladderane">ladderane</span>|Ladderane|&lt;= 3.0|7.1|
 |<span id="lanthipeptide-class-i">lanthipeptide class I</span>|Class I lanthipeptides like nisin|4.2|6.0|
 |<span id="lanthipeptide-class-ii">lanthipeptide class II</span>|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:
 |<span id="lanthipeptide-class-v">lanthipeptide class V</span>|Glycosylated lanthipeptide/linaridin hybrids like MT210103|5.1|6.0|
 |<span id="lassopeptide">lassopeptide</span>|Lasso peptide|&lt;= 3.0|5.0|
 |<span id="linaridin">linaridin</span>|Linear arid peptide such as cypemycin (HQ148718) and salinipeptin (MG788286)|&lt;= 3.0|&lt;= 3.0|
+|<span id="lincosamides">lincosamides</span>|NRPS-adjacent biosynthesis of lincosamides|8.0 beta|8.0 beta|
 |<span id="lipolanthine">lipolanthine</span>|Lanthipeptide class containing N-terminal fatty acids such as MG673929|5.0|5.0|
 |<span id="melanin">melanin</span>|Melanin|&lt;= 3.0|&lt;= 3.0|
 |<span id="methanobactin">methanobactin</span>|Copper-chelating/transporting peptides (doi:10.1126/science.aap9437)|7.0|7.0|
 |<span id="microviridin">microviridin</span>|Microviridin|&lt;= 3.0|&lt;= 3.0|
-|<span id="mycosporine-like">mycosporine-like</span>|Molecules containing mycosporine-like amino acid|7.0|7.0|
+|<span id="mycosporine">mycosporine</span>|Molecules containing mycosporine-like amino acid|7.0|8.0 beta|
 |<span id="naggn">NAGGN</span>|N-acetylglutaminylglutamine amide|5.0|5.0|
 |<span id="napaa">NAPAA</span>|Non-alpha poly-amino acids like e-Polylysin|6.0|7.0|
-|<span id="ni-siderophore"><span id="nrp-independent-siderophore">NI-siderophore</span></span>|NRPS-independent, IucA/IucC-like siderophores (*siderophore* prior to 7.0)|7.0|7.1|
-|<span id="nrps">NRPS</span>|Non-ribosomal peptide synthetase|&lt;= 3.0|6.0|
+|<span id="ni-siderophore"><span id="nrp-independent-siderophore">NI-siderophore</span></span>|NRPS-independent, IucA/IucC-like siderophores (*siderophore* prior to 7.0)|7.0|8.0 beta|
+|<span id="nitropropanoic-acid">nitropropanoic-acid</span>|3-Nitropropanoic acid (neurotoxin)|8.0 beta|8.0 beta|
+|<span id="nrps">NRPS</span>|Non-ribosomal peptide synthetase|&lt;= 3.0|8.0 beta|
 |<span id="nrp-metallophore">NRP-metallophore</span>|Non-ribosomal peptide metallophores|7.0|7.0|
 |<span id="nucleoside">nucleoside</span>|Nucleoside|&lt;= 3.0|5.0|
 |<span id="oligosaccharide">oligosaccharide</span>|Oligosaccharide|&lt;= 3.0|&lt;= 3.0|
@@ -70,6 +78,8 @@ The types of cluster within each ruleset are given below:
 |<span id="phenazine">phenazine</span>|Phenazine|&lt;= 3.0|&lt;= 3.0|
 |<span id="phosphoglycolipid">phosphoglycolipid</span>|Phosphoglycolipid|&lt;= 3.0|&lt;= 3.0|
 |<span id="phosphonate">phosphonate</span>|Phosphonate|&lt;= 3.0|7.0|
+|<span id="polyhalogenated-pyrrole">polyhalogenated-pyrrole</span>|Polyhalogenated pyrrole|8.0 beta|8.0 beta|
+|<span id="polyyne">polyyne</span>|Polyyne|8.0 beta|8.0 beta|
 |<span id="ppys-ks"><span id="ppysks">PpyS-KS</span></span>|PPY-like pyrone|4.2|4.2|
 |<span id="prodigiosin">prodigiosin</span>|Serratia-type non-traditional PKS prodigiosin biosynthesis pathway|6.0|6.0|
 |<span id="proteusin">proteusin</span>|Proteusin|&lt;= 3.0|&lt;= 3.0 |
@@ -80,42 +90,46 @@ The types of cluster within each ruleset are given below:
 |<span id="rcdps">RCDPS</span>|Fungal Arginine-containing cyclic dipeptides|7.0|7.0|
 |<span id="redox-cofactor">redox-cofactor</span>|Redox-cofactors such as PQQ (NC_021985:1458906-1494876)|6.0|6.0|
 |<span id="resorcinol">resorcinol</span>|Resorcinol|&lt;= 3.0|&lt;= 3.0|
-|<span id="saccharide">saccharide</span>|Saccharide (loose strictness, likely from primary metabolism)|&lt;= 3.0|&lt;= 3.0|
 |<span id="sactipeptide">sactipeptide</span>|Sactipeptide|&lt;= 3.0|6.0|
 |<span id="spliceotide">spliceotide</span>|RiPPs containing plpX type spliceases (NZ_KB235920:17899-42115)|6.0|6.0|
 |<span id="t1pks">T1PKS</span>|Type I PKS (Polyketide synthase)|&lt;= 3.0|&lt;= 3.0|
 |<span id="t2pks">T2PKS</span>|Type II PKS|&lt;= 3.0|5.0|
 |<span id="t3pks">T3PKS</span>|Type III PKS|&lt;= 3.0|&lt;= 3.0|
-|<span id="terpene">terpene</span>|Terpene|&lt;= 3.0|4.1|
+|<span id="terpene">terpene</span>|Terpene|&lt;= 3.0|8.0 beta|
 |<span id="thioamitides">thioamitides</span>|Thioamitide RiPPs as found in JOBF01000011|5.1|6.0|
 |<span id="thioamide-nrp">thioamide-NRP</span>|Thioamide-containing non-ribosomal peptide|5.0|5.0|
-|<span id="thiopeptide">thiopeptide</span>|Thiopeptide|4.2|5.0|
-|<span id="transatpks"><span id="transat-pks">transAT-PKS</span></span>|Trans-AT PKS|&lt;= 3.0|5.0|
+|<span id="transatpks"><span id="transat-pks">transAT-PKS</span></span>|Trans-AT PKS|&lt;= 3.0|8.0 beta|
 |<span id="triceptide">triceptide</span>|Triceptides|7.1|7.1|
 |<span id="tropodithietic-acid">tropodithietic-acid</span>|Tropodithietic acid|5.0|5.0|
 
 ### Relaxed
 |Label|Description|Added|Last updated|
 |-----|-----------|:---:|:----------:|
 |<span id="fungal-ripp-like">fungal-RiPP-like</span>|Fungal RiPP-likes|7.0|7.0|
-|<span id="nrps-like"><span id="nrpsfragment">NRPS-like</span></span>|NRPS-like fragment|5.0|5.0|
+|<span id="nrps-like"><span id="nrpsfragment">NRPS-like</span></span>|NRPS-like fragment|5.0|8.0 beta|
 |<span id="phosphonate-like">phosphonate-like</span>|Phosphonate-like (prior to 7.0 this was the phosphonate rule)|7.0|7.0|
 |<span id="pks-like">PKS-like</span>|Other types of PKS|5.0|5.0|
 |<span id="ripp-like">RiPP-like</span>|Other unspecified ribosomally synthesised and post-translationally modified peptide product (RiPP)|4.1|7.0|
 |<span id="rre-containing">RRE-containing</span>|RRE-element containing cluster|6.0|6.0|
+|<span id="terpene">terpene-precursor</span>|Compound likely used as a terpene precursor|8.0 beta|8.0 beta|
 |<span id="transatpks-like"><span id="transat-pks-like">transAT-PKS-like</span></span>|Trans-AT PKS fragment, with trans-AT domain not found|&lt;= 5.0|5.0|
 
 ### Loose
 |Label|Description|Added|Last updated|
 |-----|-----------|:---:|:----------:|
 |<span id="fatty_acid">fatty_acid</span>|Fatty acid (loose strictness, likely from primary metabolism)|&lt;= 3.0|4.2|
 |<span id="halogenated">halogenated</span>|Halogenase-containing cluster, potentially generating a halogenated product|5.0|5.0|
+|<span id="lysine">lysine</span>|Fungal lysine primary metabolism|8.0 beta|8.0 beta|
+|<span id="saccharide">saccharide</span>|Saccharide (loose strictness, likely from primary metabolism)|&lt;= 3.0|&lt;= 3.0|
 
 
 ##Obsolete/Previous Types
 
 |Label|Description|Added|Removed|Notes|
 |-----|-----------|:---:|:-----:|-----|
+|<span id="lap">LAP</span>|Linear azol(in)e-containing peptides|&lt;= 3.0|8.0 beta|Merged with *thiopeptide* into *azole-containing RiPP*|
+|<span id="mycosporine-like">mycosporine-like</span>|Molecules containing mycosporine-like amino acid|7.0|8.0 beta|Renamed to *mycosporine*|
+|<span id="thiopeptide">thiopeptide</span>|Thiopeptide|4.2|8.0 beta|Merged with *LAP* into *azole-containing RiPP*|
 |<span id="siderophore">siderophore</span>|Siderophore|&lt;= 3.0|7.0|Renamed to *NI-siderophore*|
 |<span id="bacteriocin">bacteriocin</span>|Bacteriocin or other unspecified ribosomally synthesised and <br/> post-translationally modified peptide product (RiPP)|4.1|6.0|Renamed to *RiPP-like*|
 |<span id="fused">fused</span>|Pheganomycin-style protein ligase-containing cluster|4.0|6.0|Renamed to *guanidinotides*|