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10 changes: 5 additions & 5 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,8 @@ repos:
pass_filenames: false
entry: uv lock --upgrade
language: system
- id: pytest
name: pytest
entry: uv run pytest
pass_filenames: false
language: system
# - id: pytest
# name: pytest
# entry: uv run pytest
# pass_filenames: false
# language: system
11 changes: 11 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,17 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).


## [1.22] 14-01-2026

# Added

- Data update 01/26

# Changed

- Update pre-commit (change back)

## [1.21] 19-12-2025

# Added
Expand Down
18 changes: 15 additions & 3 deletions mite_data/data/MITE0000023.json
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,17 @@
"0000-0001-6534-6609"
],
"comment": "Added cofactor information"
},
{
"version": "3",
"date": "2026-01-02",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "Added reaction description, cofactors."
}
],
"enzyme": {
Expand All @@ -38,11 +49,11 @@
"mibig": "BGC0000269"
},
"cofactors": {
"inorganic": [
"FeS"
],
"organic": [
"SAM"
],
"inorganic": [
"FeS"
]
}
},
Expand All @@ -51,6 +62,7 @@
"tailoring": [
"Methylation"
],
"description": "O-methylation of tetrycycline intermediate.",
"reactionSMARTS": "[#6:1]-[#6:2]1-[#6:38](-[#8:39])-[#6:36](-[#8:37])-[#6:35]-[#6:4](-[#6:5]2:[#6:10](-[#8:11]):[#6:9]3-[#6:12](-[#6:14]4-[#6:31](-[#6:32](-[#8:34])(-[#6:33])-[#6:8]:3:[#6:7]:[#6:6]:2)-[#6:30]-[#6:29]2-[#6:17](-[#6:19](-[#6:21](=[#6:25](-[#6:27]-2-[#8:28])-[#8:26])-[#6:22](=[#8:24])-[#7:23])=[#8:20])(-[#8:18])-[#6:15]=4-[#8:16])=[#8:13])-[#8:3]-1>>[#6]-[#8:18]-[#6:17]12-[#6:19](=[#8:20])-[#6:21](-[#6:22](-[#7:23])=[#8:24])=[#6:25](-[#8:26])-[#6:27](-[#8:28])-[#6:29]-1-[#6:30]-[#6:31]1-[#6:14](-[#6:12](=[#8:13])-[#6:9]3:[#6:8](-[#6:32]-1(-[#6:33])-[#8:34]):[#6:7]:[#6:6]:[#6:5](-[#6:4]1-[#6:35]-[#6:36](-[#8:37])-[#6:38](-[#8:39])-[#6:2](-[#6:1])-[#8:3]-1):[#6:10]:3-[#8:11])=[#6:15]-2-[#8:16]",
"reactions": [
{
Expand Down
18 changes: 15 additions & 3 deletions mite_data/data/MITE0000066.json
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,17 @@
"0000-0001-6534-6609"
],
"comment": "Homogenized enzyme descriptions"
},
{
"version": "4",
"date": "2026-01-07",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "Added reaction description, cofactor."
}
],
"enzyme": {
Expand All @@ -49,11 +60,11 @@
"mibig": "BGC0000821"
},
"cofactors": {
"inorganic": [
"Fe"
],
"organic": [
"Heme"
],
"inorganic": [
"Fe"
]
}
},
Expand All @@ -62,6 +73,7 @@
"tailoring": [
"Oxidation"
],
"description": "Oxidative cyclization of chromopyrrolic acid.",
"reactionSMARTS": "[#8:1]=[#6:2](-[#6:4]1:[#6:21](-[#6:22]2:[#6:31]3:[#6:25](:[#6:26](:[#6:28]:[#6:29]:[#6:30]:3)-[Cl:27]):[#7:24]:[#6:23]:2):[#6:10](-[#6:11]2:[#6:20]3:[#6:14](:[#6:15](:[#6:17]:[#6:18]:[#6:19]:3)-[Cl:16]):[#7:13]:[#6:12]:2):[#6:6](-[#6:7](-[#8:9])=[#8:8]):[#7:5]:1)-[#8:3]>>[#8:8]=[#6:7](-[#6:6]1:[#6:10]2:[#6:11]3:[#6:12](:[#6:23]4:[#6:22](:[#6:21]:2:[#6:4](-[#6:2](-[#8:3])=[#8:1]):[#7:5]:1):[#6:31]1:[#6:25](:[#6:26](:[#6:28]:[#6:29]:[#6:30]:1)-[Cl:27]):[#7:24]:4):[#7:13]:[#6:14]1:[#6:20]:3:[#6:19]:[#6:18]:[#6:17]:[#6:15]:1-[Cl:16])-[#8:9]",
"reactions": [
{
Expand Down
17 changes: 15 additions & 2 deletions mite_data/data/MITE0000149.json
Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,22 @@
"0000-0003-0443-9902"
],
"comment": "Initial entry. Reviewer partially fixed reactionSMARTS:reactionSMARTS, validation still not passing. Reviewer partially fixed reactions:products, validation still not passing. Reviewer 1 fixed numbering of reaction SMARTS, reaction passes."
},
{
"version": "2",
"date": "2025-12-29",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "Fixed enzyme description, added reaction description."
}
],
"enzyme": {
"name": "MciB",
"description": "P450 installing crosslink",
"description": "Cytochrome P450",
"references": [
"doi:10.1002/anie.202311533"
],
Expand All @@ -32,14 +43,16 @@
"tailoring": [
"Biaryl bond formation"
],
"description": "Macrocyclisation of Tyr-Trp via biaryl bond formation.",
"reactionSMARTS": "[#6:1]-[#6:2](-[#6:4]/[#6@@:5](-[#6:12](-[#7:14]-[#6@:15](-[#6:17](-[#7:19]-[#6:20]-[#6:21](-[#7:23]-[#6@:24](-[#6:26](-[#7:28]\\[#6@:29](-[#6:38](-[#7:40]1-[#6@:44](/[#6:45](-[#7:47]/[#6@:48](-[#6:59](-[#7:61]/[#6@:62](-[#6:69](-[#8:71])=[#8:70])-[#6:63]-[#6:64]2:[nH:68]:[#6:67]:[#7:66]:[#6:65]:2)=[#8:60])-[#6:49]-[#6:50]2:[#6:58]3:[#6:53](:[#6:54]:[#6:55]:[#6:56]:[#6:57]:3):[nH:52]:[#6:51]:2)=[#8:46])-[#6:43]-[#6:42]-[#6:41]-1)=[#8:39])-[#6:30]-[#6:31]1:[#6:37]:[#6:36]:[#6:34](-[#8:35]):[#6:33]:[#6:32]:1)=[#8:27])\\[#6:25])=[#8:22])=[#8:18])\\[#6:16])=[#8:13])-[#7:6]-[#6:7](-[#6@@:9](/[#7:11])-[#6:10])=[#8:8])-[#6:3]>>[#6:3]-[#6:2](-[#6:4]/[#6@@:5](-[#6:12](-[#7:14]-[#6@:15](-[#6:17](-[#7:19]-[#6:20]-[#6:21](-[#7:23]-[#6@:24](-[#6:26](-[#7:28]\\[#6@@:29]1-[#6:38](-[#7:40]2-[#6@:44](/[#6:45](-[#7:47]/[#6@:48](-[#6:59](-[#7:61]/[#6@:62](-[#6:69](-[#8:71])=[#8:70])-[#6:63]-[#6:64]3:[nH:68]:[#6:67]:[#7:66]:[#6:65]:3)=[#8:60])-[#6:49]-[#6:50]3:[#6:58]4:[#6:53](:[#6:54]:[#6:55]:[#6:56](-[#6:33]5:[#6:32]:[#6:31](:[#6:37]:[#6:36]:[#6:34]:5-[#8:35])-[#6:30]-1):[#6:57]:4):[nH:52]:[#6:51]:3)=[#8:46])-[#6:43]-[#6:42]-[#6:41]-2)=[#8:39])=[#8:27])\\[#6:25])=[#8:22])=[#8:18])\\[#6:16])=[#8:13])-[#7:6]-[#6:7](-[#6@@:9](/[#7:11])-[#6:10])=[#8:8])-[#6:1]",
"reactions": [
{
"substrate": "CC(C)C[C@H](NC(=O)[C@H](C)N)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)O",
"products": [
"CC(C)C[C@H](NC(=O)[C@H](C)N)C(=O)N[C@@H](C)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@H]1Cc2ccc(O)c(c2)-c2ccc3[nH]cc(c3c2)C[C@@H](C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)O)NC(=O)[C@@H]2CCCN2C1=O"
],
"isIntermediate": false
"isIntermediate": false,
"description": "Macrocyclisation of the MciA precursor peptide."
}
],
"evidence": {
Expand Down
15 changes: 13 additions & 2 deletions mite_data/data/MITE0000225.json
Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,22 @@
"0000-0003-4819-2251"
],
"comment": "new entry. Reviewer 1 adjusted reaction SMARTS to include minimally required leader and follower sequences and updated examples."
},
{
"version": "2",
"date": "2025-12-21",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "Fixed captialization of enzyme description."
}
],
"enzyme": {
"name": "ArbB2",
"description": "burpitide cyclases/BURP-domain peptide cyclases",
"description": "Burpitide cyclases/BURP-domain peptide cyclases",
"references": [
"doi:10.1021/jacs.4c15470"
],
Expand Down Expand Up @@ -68,4 +79,4 @@
}
}
]
}
}
73 changes: 73 additions & 0 deletions mite_data/data/MITE0000229.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
{
"accession": "MITE0000229",
"status": "active",
"comment": "Enzyme identifier was found by manual search for precursor peptide in genome of Brevibacillus gelatini strain DSM 100115",
"changelog": [
{
"version": "1",
"date": "2025-12-28",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "New entry."
}
],
"enzyme": {
"name": "GelC",
"description": "Macrolactam synthetase",
"references": [
"doi:10.64898/2025.12.02.691826",
"doi:10.1002/anie.202425134"
],
"auxiliaryEnzymes": [
{
"name": "GelB1",
"description": "Stand-alone ribosomal recognition element",
"databaseIds": {
"uniprot": "UPI000F0895EA"
}
},
{
"name": "GelB2",
"description": " Lassopeptide cysteine protease",
"databaseIds": {
"uniprot": "UPI000F088A46"
}
}
],
"databaseIds": {
"uniprot": "UPI000F08A2CC"
}
},
"reactions": [
{
"tailoring": [
"Macrolactam formation"
],
"description": "Lasso macrocyclisation of gelatinamin intermediate after leader peptide cleavage.",
"reactionSMARTS": "[#6:1]-[#6:2](/[#6@@:4](-[#6:105](-[#7:107]\\[#6@:108](-[#6:114](-[#7:116]/[#6@:117](-[#6:123](-[#7:125]-[#6:126]-[#6:127](-[#8:129])=[#8:128])=[#8:124])-[#6:118]-[#6:119]-[#6:120]-[#6:121]-[#7:122])=[#8:115])-[#6:109]-[#6:110]-[#6:111]-[#6:112]-[#7:113])=[#8:106])-[#7:5]-[#6:6](-[#6:8]-[#7:9]-[#6:10](/[#6@@:12](-[#7:20]-[#6:21](-[#6:23]-[#7:24]-[#6:25](\\[#6@@:27](-[#7:34]-[#6:35](\\[#6@@:37](-[#7:43]-[#6:44](-[#6:46]-[#7:47]-[#6:48](\\[#6@@:50](-[#7:55]-[#6:56](-[#6:58]-[#7:59]-[#6:60](/[#6@:62]1-[#7:66](-[#6:67](\\[#6@@:69](-[#7:75]-[#6:76](/[#6@@:78](-[#7:81]-[#6:82](\\[#6@@:84](-[#7:90]-[#6:91](/[#6@@:93](-[#7:99]-[#6:100](-[#6@@:102](\\[#7:104])-[#6:103])=[#8:101])-[#6:94]-[#6:95]-[#6:96]-[#6:97]-[#7:98])=[#8:92])-[#6:85]-[#6:86]-[#6:87]-[#6:88]-[#7:89])=[#8:83])-[#6:79]-[#8:80])=[#8:77])-[#6:70]-[#6:71]-[#6:72]-[#6:73]-[#7:74])=[#8:68])-[#6:65]-[#6:64]-[#6:63]-1)=[#8:61])=[#8:57])-[#6:51]-[#6:52](-[#8:54])=[#8:53])=[#8:49])=[#8:45])-[#6:38]-[#6:39]-[#6:40]-[#6:41]-[#7:42])=[#8:36])-[#6:28]-[#6:29]1:[#7:33]:[#6:32]:[#7:31]:[#6:30]:1)=[#8:26])=[#8:22])-[#6:13]-[#6:14]-[#6:15]-[#7:16]-[#6:17](-[#7:19])=[#7:18])=[#8:11])=[#8:7])-[#6:3]>>[#6:3]-[#6:2](/[#6@@:4](-[#6:105](-[#7:107]\\[#6@:108](-[#6:114](-[#7:116]/[#6@:117](-[#6:123](-[#7:125]-[#6:126]-[#6:127](-[#8:129])=[#8:128])=[#8:124])-[#6:118]-[#6:119]-[#6:120]-[#6:121]-[#7:122])=[#8:115])-[#6:109]-[#6:110]-[#6:111]-[#6:112]-[#7:113])=[#8:106])-[#7:5]-[#6:6](-[#6:8]-[#7:9]-[#6:10](/[#6@@:12](-[#7:20]-[#6:21](-[#6:23]-[#7:24]-[#6:25](\\[#6@@:27](-[#7:34]-[#6:35](\\[#6@@:37](-[#7:43]-[#6:44](-[#6:46]-[#7:47]-[#6:48](\\[#6@:50]1-[#7:55]-[#6:56](-[#6:58]-[#7:59]-[#6:60](/[#6@:62]2-[#7:66](-[#6:67](\\[#6@@:69](-[#7:75]-[#6:76](/[#6@@:78](-[#7:81]-[#6:82](\\[#6@@:84](-[#7:90]-[#6:91](/[#6@@:93](-[#7:99]-[#6:100](-[#6@@:102](\\[#7:104]-[#6:52](=[#8:53])-[#6:51]-1)-[#6:103])=[#8:101])-[#6:94]-[#6:95]-[#6:96]-[#6:97]-[#7:98])=[#8:92])-[#6:85]-[#6:86]-[#6:87]-[#6:88]-[#7:89])=[#8:83])-[#6:79]-[#8:80])=[#8:77])-[#6:70]-[#6:71]-[#6:72]-[#6:73]-[#7:74])=[#8:68])-[#6:65]-[#6:64]-[#6:63]-2)=[#8:61])=[#8:57])=[#8:49])=[#8:45])-[#6:38]-[#6:39]-[#6:40]-[#6:41]-[#7:42])=[#8:36])-[#6:28]-[#6:29]1:[#7:33]:[#6:32]:[#7:31]:[#6:30]:1)=[#8:26])=[#8:22])-[#6:13]-[#6:14]-[#6:15]-[#7:16]-[#6:17](-[#7:19])=[#7:18])=[#8:11])=[#8:7])-[#6:1]",
"reactions": [
{
"substrate": "CC(C)[C@H](NC(=O)CNC(=O)[C@H](CCCNC(=N)N)NC(=O)CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](CCCCN)NC(=O)CNC(=O)[C@H](CC(=O)O)NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)[C@H](C)N)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)O",
"products": [
"CC(C)[C@H](NC(=O)CNC(=O)[C@H](CCCNC(=N)N)NC(=O)CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](CCCCN)NC(=O)CNC(=O)[C@@H]1CC(=O)N[C@@H](C)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CCCCN)C(=O)N2CCC[C@H]2C(=O)NCC(=O)N1)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)O"
],
"isIntermediate": true,
"description": "Folds precursor peptide into immature Gelatinamin B"
}
],
"evidence": {
"evidenceCode": [
"Heterologous expression",
"Knock-out studies"
],
"references": [
"doi:10.64898/2025.12.02.691826"
]
}
}
]
}
73 changes: 73 additions & 0 deletions mite_data/data/MITE0000230.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
{
"accession": "MITE0000230",
"status": "active",
"comment": "Enzyme identifier was found by manual search for precursor peptide in genome of Brevibacillus gelatini strain DSM 100115",
"changelog": [
{
"version": "1",
"date": "2025-12-28",
"contributors": [
"AAAAAAAAAAAAAAAAAAAAAAAA"
],
"reviewers": [
"0000-0001-6534-6609"
],
"comment": "New entry."
}
],
"enzyme": {
"name": "GelB2",
"description": "Peptidase",
"references": [
"doi:10.1002/anie.202425134",
"doi:10.64898/2025.12.02.691826"
],
"auxiliaryEnzymes": [
{
"name": "GelB1",
"description": "Stand-alone ribosomal recognition element",
"databaseIds": {
"uniprot": "UPI000F0895EA"
}
},
{
"name": "GelC",
"description": "Macrolactam synthetase",
"databaseIds": {
"uniprot": "UPI000F08A2CC"
}
}
],
"databaseIds": {
"uniprot": "UPI000F088A46"
}
},
"reactions": [
{
"tailoring": [
"Hydrolysis"
],
"description": "N-terminal cleavage of gelatinamin leader peptide, resulting in immature intermediate core peptide.",
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"reactions": [
{
"substrate": "CSCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](CCCCN)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](N)CCSC)C(C)C)C(C)C)[C@@H](C)O)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CCCCN)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CCCCN)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)NCC(=O)N[C@@H](CCCNC(=N)N)C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)O)C(C)C)[C@@H](C)O)C(C)C",
"products": [
"CC(C)[C@H](NC(=O)CNC(=O)[C@H](CCCNC(=N)N)NC(=O)CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](CCCCN)NC(=O)CNC(=O)[C@H](CC(=O)O)NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)[C@H](C)N)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)O"
],
"isIntermediate": true,
"description": "Precursor cleavage of the GelA precursor peptide, resulting in the intermediate core peptide before macrolactam formation."
}
],
"evidence": {
"evidenceCode": [
"Heterologous expression",
"Knock-out studies"
],
"references": [
"doi:10.64898/2025.12.02.691826"
]
}
}
]
}
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