From 710fc8586934865b87cca13af88175e748efe50a Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:23:09 +0100 Subject: [PATCH 1/7] Add submission UUID file --- .../ccef9780-13ac-11f1-8244-9f391af45cf2.json | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json diff --git a/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json b/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json new file mode 100644 index 0000000..fd32a47 --- /dev/null +++ b/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json @@ -0,0 +1,79 @@ +{ + "accession": "MITE0000097", + "status": "pending", + "changelog": [ + { + "version": "1", + "date": "2024-07-30", + "contributors": [ + "0000-0003-1763-2525", + "0009-0008-3623-3734", + "AAAAAAAAAAAAAAAAAAAAAAAA" + ], + "reviewers": [ + "0000-0001-6534-6609", + "0000-0003-0443-9902" + ], + "comment": "Initial entry. Reviewer partially fixed reactions:substrate, validation still not passing. Reviewer partially fixed reactions:products, validation still not passing. Reviewer 2 reworked reaction SMARTS, reaction passes." + }, + { + "version": "2", + "date": "2025-10-27", + "contributors": [ + "AAAAAAAAAAAAAAAAAAAAAAAA" + ], + "reviewers": [ + "0000-0001-6534-6609" + ], + "comment": "Replaced retired UniProtKB ID with UniParc ID" + }, + { + "version": "3", + "date": "2026-02-27", + "contributors": [ + "AAAAAAAAAAAAAAAAAAAAAAAA" + ], + "reviewers": [ + "BBBBBBBBBBBBBBBBBBBBBBBB" + ], + "comment": "" + } + ], + "enzyme": { + "name": "PumI", + "description": "Oxidoreductase", + "references": [ + "doi:10.1016/j.chembiol.2018.02.008" + ], + "databaseIds": { + "uniprot": "UPI000D213889", + "genpept": "AVT42378.1", + "mibig": "BGC0001476" + } + }, + "reactions": [ + { + "tailoring": [ + "Oxidation" + ], + "reactionSMARTS": "[#8:1]-[#6:2]/[#6@@:3]1-[#6@@:8](\\[#8:9])-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-1>>[#8:9]\\[#6@:8]1-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-[#6@@:3]-1/[#6:2]=[#8:1]", + "reactions": [ + { + "substrate": "O=c1[nH]cc([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[nH]1", + "products": [ + "O=C[C@H]1O[C@@H](c2c[nH]c(=O)[nH]c2=O)[C@H](O)[C@@H]1O" + ], + "isIntermediate": false + } + ], + "evidence": { + "evidenceCode": [ + "Knock-out studies" + ], + "references": [ + "doi:10.1016/j.chembiol.2018.02.008" + ] + } + } + ] +} \ No newline at end of file From 4d74e95d06d98ddcbfa5db7b221fec301eaedf66 Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:23:11 +0100 Subject: [PATCH 2/7] Update entry MITE0000097 --- mite_data/data/MITE0000097.json | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/mite_data/data/MITE0000097.json b/mite_data/data/MITE0000097.json index e0c1589..fd32a47 100644 --- a/mite_data/data/MITE0000097.json +++ b/mite_data/data/MITE0000097.json @@ -1,6 +1,6 @@ { "accession": "MITE0000097", - "status": "active", + "status": "pending", "changelog": [ { "version": "1", @@ -26,6 +26,17 @@ "0000-0001-6534-6609" ], "comment": "Replaced retired UniProtKB ID with UniParc ID" + }, + { + "version": "3", + "date": "2026-02-27", + "contributors": [ + "AAAAAAAAAAAAAAAAAAAAAAAA" + ], + "reviewers": [ + "BBBBBBBBBBBBBBBBBBBBBBBB" + ], + "comment": "" } ], "enzyme": { From e0723d7e3a71f9c4dab998ec65dcd6bdc37b6191 Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:27:49 +0100 Subject: [PATCH 3/7] Update submission --- mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json b/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json index fd32a47..ee43643 100644 --- a/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json +++ b/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json @@ -36,7 +36,7 @@ "reviewers": [ "BBBBBBBBBBBBBBBBBBBBBBBB" ], - "comment": "" + "comment": "Added reaction description, changed tailoring term from oxidation to dehydrogenation." } ], "enzyme": { @@ -54,8 +54,9 @@ "reactions": [ { "tailoring": [ - "Oxidation" + "Dehydrogenation" ], + "description": "Dehydrogenates (oxidates) pseudouridine in the pseudouridimycin pathway.", "reactionSMARTS": "[#8:1]-[#6:2]/[#6@@:3]1-[#6@@:8](\\[#8:9])-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-1>>[#8:9]\\[#6@:8]1-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-[#6@@:3]-1/[#6:2]=[#8:1]", "reactions": [ { @@ -63,7 +64,8 @@ "products": [ "O=C[C@H]1O[C@@H](c2c[nH]c(=O)[nH]c2=O)[C@H](O)[C@@H]1O" ], - "isIntermediate": false + "isIntermediate": true, + "description": "Dehydrogenates pseudouridine to pseudouridine aldehyde." } ], "evidence": { From 7a72db1e5c6940ccaa0c714e99645e69d66f07c5 Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:27:50 +0100 Subject: [PATCH 4/7] Update submission --- mite_data/data/MITE0000097.json | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/mite_data/data/MITE0000097.json b/mite_data/data/MITE0000097.json index fd32a47..ee43643 100644 --- a/mite_data/data/MITE0000097.json +++ b/mite_data/data/MITE0000097.json @@ -36,7 +36,7 @@ "reviewers": [ "BBBBBBBBBBBBBBBBBBBBBBBB" ], - "comment": "" + "comment": "Added reaction description, changed tailoring term from oxidation to dehydrogenation." } ], "enzyme": { @@ -54,8 +54,9 @@ "reactions": [ { "tailoring": [ - "Oxidation" + "Dehydrogenation" ], + "description": "Dehydrogenates (oxidates) pseudouridine in the pseudouridimycin pathway.", "reactionSMARTS": "[#8:1]-[#6:2]/[#6@@:3]1-[#6@@:8](\\[#8:9])-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-1>>[#8:9]\\[#6@:8]1-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-[#6@@:3]-1/[#6:2]=[#8:1]", "reactions": [ { @@ -63,7 +64,8 @@ "products": [ "O=C[C@H]1O[C@@H](c2c[nH]c(=O)[nH]c2=O)[C@H](O)[C@@H]1O" ], - "isIntermediate": false + "isIntermediate": true, + "description": "Dehydrogenates pseudouridine to pseudouridine aldehyde." } ], "evidence": { From 8a58b74c5572364042eea0f3c73d741d80d73b7c Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:29:42 +0100 Subject: [PATCH 5/7] Delete mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json --- .../ccef9780-13ac-11f1-8244-9f391af45cf2.json | 81 ------------------- 1 file changed, 81 deletions(-) delete mode 100644 mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json diff --git a/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json b/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json deleted file mode 100644 index ee43643..0000000 --- a/mite_data/data/ccef9780-13ac-11f1-8244-9f391af45cf2.json +++ /dev/null @@ -1,81 +0,0 @@ -{ - "accession": "MITE0000097", - "status": "pending", - "changelog": [ - { - "version": "1", - "date": "2024-07-30", - "contributors": [ - "0000-0003-1763-2525", - "0009-0008-3623-3734", - "AAAAAAAAAAAAAAAAAAAAAAAA" - ], - "reviewers": [ - "0000-0001-6534-6609", - "0000-0003-0443-9902" - ], - "comment": "Initial entry. Reviewer partially fixed reactions:substrate, validation still not passing. Reviewer partially fixed reactions:products, validation still not passing. Reviewer 2 reworked reaction SMARTS, reaction passes." - }, - { - "version": "2", - "date": "2025-10-27", - "contributors": [ - "AAAAAAAAAAAAAAAAAAAAAAAA" - ], - "reviewers": [ - "0000-0001-6534-6609" - ], - "comment": "Replaced retired UniProtKB ID with UniParc ID" - }, - { - "version": "3", - "date": "2026-02-27", - "contributors": [ - "AAAAAAAAAAAAAAAAAAAAAAAA" - ], - "reviewers": [ - "BBBBBBBBBBBBBBBBBBBBBBBB" - ], - "comment": "Added reaction description, changed tailoring term from oxidation to dehydrogenation." - } - ], - "enzyme": { - "name": "PumI", - "description": "Oxidoreductase", - "references": [ - "doi:10.1016/j.chembiol.2018.02.008" - ], - "databaseIds": { - "uniprot": "UPI000D213889", - "genpept": "AVT42378.1", - "mibig": "BGC0001476" - } - }, - "reactions": [ - { - "tailoring": [ - "Dehydrogenation" - ], - "description": "Dehydrogenates (oxidates) pseudouridine in the pseudouridimycin pathway.", - "reactionSMARTS": "[#8:1]-[#6:2]/[#6@@:3]1-[#6@@:8](\\[#8:9])-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-1>>[#8:9]\\[#6@:8]1-[#6@@:6](\\[#8:7])-[#6@:5](/[#6:10]2:[#6:16](=[#8:17]):[#7:15]:[#6:13](=[#8:14]):[#7:12]:[#6:11]:2)-[#8:4]-[#6@@:3]-1/[#6:2]=[#8:1]", - "reactions": [ - { - "substrate": "O=c1[nH]cc([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[nH]1", - "products": [ - "O=C[C@H]1O[C@@H](c2c[nH]c(=O)[nH]c2=O)[C@H](O)[C@@H]1O" - ], - "isIntermediate": true, - "description": "Dehydrogenates pseudouridine to pseudouridine aldehyde." - } - ], - "evidence": { - "evidenceCode": [ - "Knock-out studies" - ], - "references": [ - "doi:10.1016/j.chembiol.2018.02.008" - ] - } - } - ] -} \ No newline at end of file From 8af0bbaaa99e98b99c6f3ffc895d03e9dd9d4034 Mon Sep 17 00:00:00 2001 From: mite-bot Date: Fri, 27 Feb 2026 08:29:44 +0100 Subject: [PATCH 6/7] Update submission --- mite_data/data/MITE0000097.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mite_data/data/MITE0000097.json b/mite_data/data/MITE0000097.json index ee43643..087f785 100644 --- a/mite_data/data/MITE0000097.json +++ b/mite_data/data/MITE0000097.json @@ -1,6 +1,6 @@ { "accession": "MITE0000097", - "status": "pending", + "status": "active", "changelog": [ { "version": "1", @@ -34,7 +34,7 @@ "AAAAAAAAAAAAAAAAAAAAAAAA" ], "reviewers": [ - "BBBBBBBBBBBBBBBBBBBBBBBB" + "0000-0001-6534-6609" ], "comment": "Added reaction description, changed tailoring term from oxidation to dehydrogenation." } From 0807bf6faecefef91f9c9324afb73591e8a15c08 Mon Sep 17 00:00:00 2001 From: "Mitja M. Zdouc" <95709447+mmzdouc@users.noreply.github.com> Date: Fri, 27 Feb 2026 08:43:43 +0100 Subject: [PATCH 7/7] Update MITE0000097.json Removed MIBiG reference: does not exist in MIBiG 4.0 --- mite_data/data/MITE0000097.json | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/mite_data/data/MITE0000097.json b/mite_data/data/MITE0000097.json index 087f785..fb43e69 100644 --- a/mite_data/data/MITE0000097.json +++ b/mite_data/data/MITE0000097.json @@ -47,8 +47,7 @@ ], "databaseIds": { "uniprot": "UPI000D213889", - "genpept": "AVT42378.1", - "mibig": "BGC0001476" + "genpept": "AVT42378.1" } }, "reactions": [ @@ -78,4 +77,4 @@ } } ] -} \ No newline at end of file +}