ARBA rule assigning the pathway comment "Pyrimidine metabolism; UMP biosynthesis via de novo pathway" through 26 alternative condition sets built from InterPro, CATH FunFam, PANTHER and taxon conditions.
Condition-set counts describe the sets recorded in this review, which may omit the full rule.
No domain overlap table is shown: the cached overlap analysis for this version of the review is not available.
Run just analyze-rule ARBA00004725 and re-render to add it.
All 26 live condition sets are recorded with their official labels. By those labels the InterPro sets name dihydroorotate dehydrogenase, orotidine 5'-phosphate decarboxylase, orotate phosphoribosyltransferase, aspartate carbamoyltransferase and dihydroorotase families, which are enzymes of de novo UMP biosynthesis. The sets were not checked against the curated pathway comments of their Swiss-Prot members, so no verdict is given. UniProt reports 7889 unreviewed proteins for the rule.
The condition sets were read but not checked against annotated proteins. No wrongly annotated protein is known.
matched_protein_count is the unreviewedProteinCount from rest.uniprot.org/arba/ARBA00004725 on 2026-11-09. InterPro API names: IPR005720 Dihydroorotate dehydrogenase, catalytic; IPR012135 Dihydroorotate dehydrogenase, class 1/ 2; IPR001754 Orotidine 5'-phosphate decarboxylase domain; IPR014732 and IPR011995 Orotidine 5'-phosphate decarboxylase families; IPR023031 Orotate phosphoribosyltransferase; IPR002082 Aspartate carbamoyltransferase; IPR004721 Dihydroorotase homodimeric type. No matched protein was checked.
id: ARBA00004725
description: >-
ARBA rule assigning the pathway comment "Pyrimidine metabolism; UMP biosynthesis via de novo pathway"
through 26 alternative condition sets built from InterPro, CATH FunFam, PANTHER and taxon conditions.
status: IN_PROGRESS
rule_type: ARBA
rule:
rule_id: ARBA00004725
condition_sets:
- number: 1
conditions:
- condition_type: INTERPRO
value: IPR005720
curie: InterPro:IPR005720
label: Dihydroorotate dehydrogenase, catalytic
negated: false
- condition_type: INTERPRO
value: IPR013785
curie: InterPro:IPR013785
label: Aldolase-type TIM barrel
negated: false
- condition_type: INTERPRO
value: IPR050074
curie: InterPro:IPR050074
label: Dihydroorotate dehydrogenase
negated: false
- number: 2
conditions:
- condition_type: INTERPRO
value: IPR012135
curie: InterPro:IPR012135
label: Dihydroorotate dehydrogenase, class 1/ 2
negated: false
- number: 3
conditions:
- condition_type: INTERPRO
value: IPR001754
curie: InterPro:IPR001754
label: Orotidine 5'-phosphate decarboxylase domain
negated: false
- condition_type: INTERPRO
value: IPR011060
curie: InterPro:IPR011060
label: Ribulose-phosphate binding barrel
negated: false
- condition_type: INTERPRO
value: IPR018089
curie: InterPro:IPR018089
label: Orotidine 5'-phosphate decarboxylase, active site
negated: false
- number: 4
conditions:
- condition_type: INTERPRO
value: IPR014732
curie: InterPro:IPR014732
label: Orotidine 5'-phosphate decarboxylase
negated: false
- number: 5
conditions:
- condition_type: INTERPRO
value: IPR000836
curie: InterPro:IPR000836
label: Phosphoribosyltransferase domain
negated: false
- condition_type: INTERPRO
value: IPR023031
curie: InterPro:IPR023031
label: Orotate phosphoribosyltransferase
negated: false
- condition_type: INTERPRO
value: IPR029057
curie: InterPro:IPR029057
label: Phosphoribosyltransferase-like
negated: false
- number: 6
conditions:
- condition_type: PANTHER
value: PTHR19278
curie: PANTHER:PTHR19278
label: OROTATE PHOSPHORIBOSYLTRANSFERASE
negated: false
- condition_type: PANTHER
value: PTHR19278:SF9
curie: PANTHER:PTHR19278:SF9
label: URIDINE 5'-MONOPHOSPHATE SYNTHASE
negated: false
- number: 7
conditions:
- condition_type: INTERPRO
value: IPR002082
curie: InterPro:IPR002082
label: Aspartate carbamoyltransferase
negated: false
- condition_type: INTERPRO
value: IPR006130
curie: InterPro:IPR006130
label: Aspartate/ornithine carbamoyltransferase
negated: false
- condition_type: INTERPRO
value: IPR006131
curie: InterPro:IPR006131
label: Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain
negated: false
- number: 8
conditions:
- condition_type: INTERPRO
value: IPR011995
curie: InterPro:IPR011995
label: Orotidine 5'-phosphate decarboxylase, type 2
negated: false
- number: 9
conditions:
- condition_type: INTERPRO
value: IPR004721
curie: InterPro:IPR004721
label: Dihydroorotase homodimeric type
negated: false
- condition_type: INTERPRO
value: IPR006680
curie: InterPro:IPR006680
label: Amidohydrolase-related
negated: false
- condition_type: PANTHER
value: PTHR43137:SF1
curie: PANTHER:PTHR43137:SF1
label: DIHYDROOROTASE
negated: false
- number: 10
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000114
curie: CATH.FunFam:3.20.20.70:FF:000114
label: Decarboxylase,orotidine phosphate
negated: false
- condition_type: TAXON
value: Eukaryota
label: Eukaryota
negated: false
- number: 11
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000069
curie: CATH.FunFam:3.20.20.70:FF:000069
negated: false
- condition_type: TAXON
value: Bacteria
label: Bacteria
negated: false
- number: 12
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000027
curie: CATH.FunFam:3.20.20.70:FF:000027
label: Dihydropyrimidine dehydrogenase [NADP(+)]
negated: false
- condition_type: TAXON
value: Bacillati
label: Bacillati
negated: false
- number: 13
conditions:
- condition_type: FUNFAM
value: 3.40.50.1370:FF:000002
curie: CATH.FunFam:3.40.50.1370:FF:000002
label: Aspartate carbamoyltransferase 2
negated: false
- number: 14
conditions:
- condition_type: FUNFAM
value: 3.40.50.2020:FF:000008
curie: CATH.FunFam:3.40.50.2020:FF:000008
label: Orotate phosphoribosyltransferase
negated: false
- condition_type: TAXON
value: Fungi
label: Fungi
negated: false
- number: 15
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000066
curie: CATH.FunFam:3.20.20.70:FF:000066
label: Dihydroorotate dehydrogenase (quinone), mitochondrial
negated: false
- number: 16
conditions:
- condition_type: FUNFAM
value: 3.40.50.2020:FF:000025
curie: CATH.FunFam:3.40.50.2020:FF:000025
label: Uridine monophosphate synthetase
negated: false
- number: 17
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000028
curie: CATH.FunFam:3.20.20.70:FF:000028
negated: false
- condition_type: TAXON
value: Pseudomonadati
label: Pseudomonadati
negated: false
- number: 18
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000123
curie: CATH.FunFam:3.20.20.70:FF:000123
negated: false
- number: 19
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000246
curie: CATH.FunFam:3.20.20.70:FF:000246
negated: false
- number: 20
conditions:
- condition_type: FUNFAM
value: 3.20.20.140:FF:000006
curie: CATH.FunFam:3.20.20.140:FF:000006
negated: false
- number: 21
conditions:
- condition_type: FUNFAM
value: 3.50.30.20:FF:000001
curie: CATH.FunFam:3.50.30.20:FF:000001
label: Carbamoyl-phosphate synthase small chain
negated: false
- number: 22
conditions:
- condition_type: FUNFAM
value: 2.10.240.10:FF:000001
curie: CATH.FunFam:2.10.240.10:FF:000001
negated: false
- condition_type: TAXON
value: Bacillota
label: Bacillota
negated: false
- number: 23
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000339
curie: CATH.FunFam:3.20.20.70:FF:000339
negated: false
- condition_type: TAXON
value: Thermotogati
label: Thermotogati
negated: false
- number: 24
conditions:
- condition_type: FUNFAM
value: 3.40.50.20:FF:000001
curie: CATH.FunFam:3.40.50.20:FF:000001
label: Carbamoyl-phosphate synthase large chain
negated: false
- condition_type: TAXON
value: Archaea
label: Archaea
negated: false
- number: 25
conditions:
- condition_type: FUNFAM
value: 3.20.20.140:FF:000041
curie: CATH.FunFam:3.20.20.140:FF:000041
negated: false
- number: 26
conditions:
- condition_type: FUNFAM
value: 3.20.20.70:FF:000015
curie: CATH.FunFam:3.20.20.70:FF:000015
negated: false
go_annotations: []
entries: []
reviewed_protein_count: 0
unreviewed_protein_count: 7889
created_date: '2020-05-12'
modified_date: '2026-07-18'
retrieved_date: '2026-11-09'
source_condition_set_count: 26
review_summary: >-
All 26 live condition sets are recorded with their official labels. By those labels the InterPro
sets name dihydroorotate dehydrogenase, orotidine 5'-phosphate decarboxylase, orotate phosphoribosyltransferase,
aspartate carbamoyltransferase and dihydroorotase families, which are enzymes of de novo UMP biosynthesis.
The sets were not checked against the curated pathway comments of their Swiss-Prot members, so no
verdict is given. UniProt reports 7889 unreviewed proteins for the rule.
action: UNDECIDED
action_rationale: >-
The condition sets were read but not checked against annotated proteins. No wrongly annotated protein
is known.
suggested_modifications:
- Check each condition set against the curated PATHWAY comment of its Swiss-Prot members.
annotation_assessments:
- annotation_kind: OTHER
value: 'PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway'
assessment: UNDECIDED
matched_protein_count: 7889
notes: >-
matched_protein_count is the unreviewedProteinCount from rest.uniprot.org/arba/ARBA00004725 on
2026-11-09. InterPro API names: IPR005720 Dihydroorotate dehydrogenase, catalytic; IPR012135 Dihydroorotate
dehydrogenase, class 1/ 2; IPR001754 Orotidine 5'-phosphate decarboxylase domain; IPR014732 and
IPR011995 Orotidine 5'-phosphate decarboxylase families; IPR023031 Orotate phosphoribosyltransferase;
IPR002082 Aspartate carbamoyltransferase; IPR004721 Dihydroorotase homodimeric type. No matched
protein was checked.
corrections:
- date: '2026-11-10'
withdrawn_claim: >-
The rule should add specific GO molecular function terms for each enzyme (for example dihydroorotate
dehydrogenase activity).
correction: >-
A rule gives the same annotation to every protein it matches. This rule matches six different
enzymes, so an enzyme-specific term added to it would be wrong for the other five. The shared
pathway comment is the statement that holds for all of them.
error_type: OTHER
evidence:
- 'Live set 1: IPR005720 AND IPR013785 AND IPR050074 (dihydroorotate dehydrogenase)'
- 'Live set 3: IPR001754 AND IPR011060 AND IPR018089 (orotidine 5''-phosphate decarboxylase)'
- 'Live set 7: IPR002082 AND IPR006130 AND IPR006131 (aspartate carbamoyltransferase)'
- date: '2026-11-10'
withdrawn_claim: Bacillati and Pseudomonadati are very narrow taxonomic scopes.
correction: Both are kingdom-rank bacterial taxa.
error_type: TAXON_MISREAD
evidence:
- 'UniProt taxonomy 1783272 Bacillati: rank kingdom'
- 'UniProt taxonomy 3379134 Pseudomonadati: rank kingdom'
- date: '2026-11-10'
withdrawn_claim: Conditions 1, 2, 3, 12, 16, 18, 19, 20 and 24 all target dihydroorotate dehydrogenase.
correction: >-
Set 3 is an orotidine 5'-phosphate decarboxylase signature, and the previous text also listed
condition 20 under orotidine 5'-phosphate decarboxylase. The overlap claim was not measured.
error_type: WRONG_IDENTIFIER_MEANING
evidence:
- 'InterPro API: IPR001754 = Orotidine 5''-phosphate decarboxylase domain'
- date: '2026-11-10'
withdrawn_claim: 27 condition sets exceed a recommended maximum of 12, so the rule needs consolidation.
correction: >-
Rule size is not evidence about correctness; a pathway with six enzymes needs several alternative
conditions. The live rule has 26 sets.
error_type: SIZE_AS_EVIDENCE
evidence:
- 'rest.uniprot.org/arba/ARBA00004725, 2026-11-09: 26 sets'