ARBA00047244 obsolete amide catabolic process (GO:0043605)

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: DEPRECATE
Confidence: 0.90

Description

ARBA rule that assigned GO:0043605 amide catabolic process through four condition sets: urease signatures, PM20D1 FunFams in Eukaryota, ureide-pathway hydrolase FunFams in Viridiplantae, and an (S)-ureidoglycine aminohydrolase FunFam in Streptophyta. UniProt no longer serves the rule and the GO term is obsolete.

Analysis Summary

Condition-set counts describe the sets recorded in this review, which may omit the full rule.

5
Domain Pairs Analyzed
4
Recorded condition sets
1
Subset Relationships
0
Redundant Annotations

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00047244 and re-render to add it.

Review Summary

UniProt returned 404 for this rule on 2026-11-09, and GO:0043605 is now obsolete in GO. The condition sets recorded here are those of the last version reviewed and could not be re-read. Nothing found in that version showed a wrong annotation.

Action Rationale

The rule has been withdrawn by UniProt and its only consequent is an obsolete GO term.

GO Annotations

GO:0043605 - obsolete amide catabolic process
Aspect: BP

Annotation Assessments

UNDECIDED GO_TERM GO:0043605 - obsolete amide catabolic process
Matched proteins: ; incorrect:

QuickGO, 2026-11-09: GO:0043605 isObsolete = true. No matched protein was checked.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

Three urease signatures required together. The Swiss-Prot counts below are for each signature alone; few entries carry all three.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
IPR002019 IPR002026 279 308 29 0.052 0.104 0.094 LOW
IPR002019 IPR017950 279 264 10 0.019 0.036 0.038 LOW
IPR002026 IPR017950 308 264 10 0.018 0.032 0.038 LOW

Condition Set 2

3 condition(s)
Notes:

Two FunFams named for PM20D1; they match the same ten Swiss-Prot proteins.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
1.10.150.900:FF:000003 3.40.630.10:FF:000027 10 10 10 1.000 1.000 1.000 REDUNDANT

Condition Set 3

3 condition(s)
Notes:

Two FunFams named for ureidoglycolate hydrolase and allantoate amidohydrolase, in Viridiplantae.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
3.30.70.360:FF:000012 3.40.630.10:FF:000044 2 7 2 0.286 1.000 0.286 SUBSET

Condition Set 4

2 condition(s)
Notes:

One FunFam named for (S)-ureidoglycine aminohydrolase, in Streptophyta.

Assessments

MISMATCHED

The consequent GO:0043605 is obsolete.

Raw YAML

View Source YAML 
id: ARBA00047244
description: >-
  ARBA rule that assigned GO:0043605 amide catabolic process through four condition sets: urease signatures,
  PM20D1 FunFams in Eukaryota, ureide-pathway hydrolase FunFams in Viridiplantae, and an (S)-ureidoglycine
  aminohydrolase FunFam in Streptophyta. UniProt no longer serves the rule and the GO term is obsolete.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00047244
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR002019
      curie: InterPro:IPR002019
      label: Urease, beta subunit-like
      negated: false
    - condition_type: INTERPRO
      value: IPR002026
      curie: InterPro:IPR002026
      label: Urease, gamma/gamma-beta subunit
      negated: false
    - condition_type: INTERPRO
      value: IPR017950
      curie: InterPro:IPR017950
      label: Urease active site
      negated: false
    notes: >-
      Three urease signatures required together. The Swiss-Prot counts below are for each signature
      alone; few entries carry all three.
    pairwise_overlap:
    - condition_a: IPR002019
      condition_b: IPR002026
      protein_database: SWISSPROT
      count_a: 279
      count_b: 308
      intersection_count: 29
      a_minus_b_count: 250
      b_minus_a_count: 279
      jaccard_similarity: 0.05197132616487455
      containment_a_in_b: 0.1039426523297491
      containment_b_in_a: 0.09415584415584416
      interpretation: LOW
    - condition_a: IPR002019
      condition_b: IPR017950
      protein_database: SWISSPROT
      count_a: 279
      count_b: 264
      intersection_count: 10
      a_minus_b_count: 269
      b_minus_a_count: 254
      jaccard_similarity: 0.01876172607879925
      containment_a_in_b: 0.035842293906810034
      containment_b_in_a: 0.03787878787878788
      interpretation: LOW
    - condition_a: IPR002026
      condition_b: IPR017950
      protein_database: SWISSPROT
      count_a: 308
      count_b: 264
      intersection_count: 10
      a_minus_b_count: 298
      b_minus_a_count: 254
      jaccard_similarity: 0.017793594306049824
      containment_a_in_b: 0.032467532467532464
      containment_b_in_a: 0.03787878787878788
      interpretation: LOW
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 1.10.150.900:FF:000003
      curie: CATH.FunFam:1.10.150.900:FF:000003
      label: N-fatty-acyl-amino acid synthase/hydrolase PM20D1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.630.10:FF:000027
      curie: CATH.FunFam:3.40.630.10:FF:000027
      label: N-fatty-acyl-amino acid synthase/hydrolase PM20D1
      negated: false
    - condition_type: TAXON
      value: '2759'
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: Two FunFams named for PM20D1; they match the same ten Swiss-Prot proteins.
    pairwise_overlap:
    - condition_a: 1.10.150.900:FF:000003
      condition_b: 3.40.630.10:FF:000027
      protein_database: SWISSPROT
      count_a: 10
      count_b: 10
      intersection_count: 10
      a_minus_b_count: 0
      b_minus_a_count: 0
      jaccard_similarity: 1.0
      containment_a_in_b: 1.0
      containment_b_in_a: 1.0
      interpretation: REDUNDANT
  - number: 3
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.360:FF:000012
      curie: CATH.FunFam:3.30.70.360:FF:000012
      label: Putative ureidoglycolate hydrolase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.630.10:FF:000044
      curie: CATH.FunFam:3.40.630.10:FF:000044
      label: Allantoate amidohydrolase
      negated: false
    - condition_type: TAXON
      value: '33090'
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      Two FunFams named for ureidoglycolate hydrolase and allantoate amidohydrolase, in Viridiplantae.
    pairwise_overlap:
    - condition_a: 3.30.70.360:FF:000012
      condition_b: 3.40.630.10:FF:000044
      protein_database: SWISSPROT
      count_a: 2
      count_b: 7
      intersection_count: 2
      a_minus_b_count: 0
      b_minus_a_count: 5
      jaccard_similarity: 0.2857142857142857
      containment_a_in_b: 1.0
      containment_b_in_a: 0.2857142857142857
      interpretation: SUBSET
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 2.60.120.10:FF:000137
      curie: CATH.FunFam:2.60.120.10:FF:000137
      label: (S)-ureidoglycine aminohydrolase
      negated: false
    - condition_type: TAXON
      value: '35493'
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: One FunFam named for (S)-ureidoglycine aminohydrolase, in Streptophyta.
  go_annotations:
  - go_id: GO:0043605
    go_label: obsolete amide catabolic process
    aspect: BP
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2024-08-14'
  modified_date: '2025-03-21'
  entries:
  - id: 1.10.150.900:FF:000003
    type: FUNFAM
    label: N-fatty-acyl-amino acid synthase/hydrolase PM20D1
    appears_in_condition_sets:
    - 2
    protein_count: 10
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 10
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 0.7
      jaccard_similarity: 0.003
      intersection_count: 7
      exclusive_count: 3
  - id: 2.60.120.10:FF:000137
    type: FUNFAM
    label: (S)-ureidoglycine aminohydrolase
    appears_in_condition_sets:
    - 4
    protein_count: 2
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 1.0
      jaccard_similarity: 0.001
      intersection_count: 2
      exclusive_count: 0
  - id: 3.30.70.360:FF:000012
    type: FUNFAM
    label: Putative ureidoglycolate hydrolase
    appears_in_condition_sets:
    - 3
    protein_count: 2
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: PREDICTS
      target_id: 3.40.630.10:FF:000044
      containment: 1.0
      jaccard_similarity: 0.286
      intersection_count: 2
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 2
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 1.0
      jaccard_similarity: 0.001
      intersection_count: 2
      exclusive_count: 0
  - id: 3.40.630.10:FF:000027
    type: FUNFAM
    label: N-fatty-acyl-amino acid synthase/hydrolase PM20D1
    appears_in_condition_sets:
    - 2
    protein_count: 10
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 10
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 10
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 0.7
      jaccard_similarity: 0.003
      intersection_count: 7
      exclusive_count: 3
  - id: 3.40.630.10:FF:000044
    type: FUNFAM
    label: Allantoate amidohydrolase
    appears_in_condition_sets:
    - 3
    protein_count: 7
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: PREDICTED_BY
      target_id: 3.30.70.360:FF:000012
      containment: 0.286
      jaccard_similarity: 0.286
      intersection_count: 2
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 7
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 0.571
      jaccard_similarity: 0.002
      intersection_count: 4
      exclusive_count: 3
  - id: IPR002019
    type: INTERPRO
    label: Urease, beta subunit-like
    appears_in_condition_sets:
    - 1
    protein_count: 279
    related_entries:
    - relationship: PREDICTS
      target_id: IPR002026
      containment: 0.104
      jaccard_similarity: 0.052
      intersection_count: 29
      exclusive_count: 250
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.038
      jaccard_similarity: 0.019
      intersection_count: 10
      exclusive_count: 269
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 279
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 279
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 279
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 279
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 279
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 1.0
      jaccard_similarity: 0.125
      intersection_count: 279
      exclusive_count: 0
  - id: IPR002026
    type: INTERPRO
    label: Urease, gamma/gamma-beta subunit
    appears_in_condition_sets:
    - 1
    protein_count: 308
    related_entries:
    - relationship: PREDICTED_BY
      target_id: IPR002019
      containment: 0.094
      jaccard_similarity: 0.052
      intersection_count: 29
      exclusive_count: 279
    - relationship: EQUIV
      target_id: IPR017950
      containment: 0.038
      jaccard_similarity: 0.018
      intersection_count: 10
      exclusive_count: 298
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 308
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 308
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 308
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 308
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 308
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 1.0
      jaccard_similarity: 0.138
      intersection_count: 308
      exclusive_count: 0
  - id: IPR017950
    type: INTERPRO
    label: Urease active site
    appears_in_condition_sets:
    - 1
    protein_count: 264
    related_entries:
    - relationship: EQUIV
      target_id: IPR002019
      containment: 0.038
      jaccard_similarity: 0.019
      intersection_count: 10
      exclusive_count: 254
    - relationship: EQUIV
      target_id: IPR002026
      containment: 0.038
      jaccard_similarity: 0.018
      intersection_count: 10
      exclusive_count: 254
    - relationship: EQUIV
      target_id: 1.10.150.900:FF:000003
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 264
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000027
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 264
    - relationship: EQUIV
      target_id: 3.30.70.360:FF:000012
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 264
    - relationship: EQUIV
      target_id: 3.40.630.10:FF:000044
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 264
    - relationship: EQUIV
      target_id: 2.60.120.10:FF:000137
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 264
    - relationship: PREDICTS
      target_id: GO:0043605
      containment: 1.0
      jaccard_similarity: 0.118
      intersection_count: 264
      exclusive_count: 0
  retrieved_date: '2026-11-09'
  withdrawn: true
review_summary: >-
  UniProt returned 404 for this rule on 2026-11-09, and GO:0043605 is now obsolete in GO. The condition
  sets recorded here are those of the last version reviewed and could not be re-read. Nothing found
  in that version showed a wrong annotation.
action: DEPRECATE
action_rationale: The rule has been withdrawn by UniProt and its only consequent is an obsolete GO
  term.
suggested_modifications:
- 'No change to make: the rule is withdrawn.'
go_specificity:
  assessment: MISMATCHED
  notes: The consequent GO:0043605 is obsolete.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0043605
  label: obsolete amide catabolic process
  assessment: UNDECIDED
  consequent_obsolete: true
  notes: 'QuickGO, 2026-11-09: GO:0043605 isObsolete = true. No matched protein was checked.'
confidence: 0.9
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Requiring three urease signatures together is a logical error because it gives a 99% false negative
    rate.
  correction: >-
    Matching fewer proteins is not an error in the annotation. A conjunction that selects only proteins
    with all three signatures is narrower, and the previous text itself found every signature fully
    contained in the annotated set. The total of 851 urease proteins was the sum of three overlapping
    counts.
  error_type: LOW_RECALL_IS_NOT_WRONG
  evidence:
  - >-
    Recorded Swiss-Prot counts: IPR002019 279, IPR002026 308, IPR017950 264; pairwise intersections
    29, 10, 10
- date: '2026-11-10'
  withdrawn_claim: >-
    The two PM20D1 FunFams are redundant and set 3 misses five allantoate amidohydrolase proteins,
    which invalidates the rule.
  correction: Redundant or narrow conditions do not make the annotation wrong.
  error_type: LOW_RECALL_IS_NOT_WRONG
  evidence:
  - >-
    Recorded Swiss-Prot counts: both PM20D1 FunFams 10 of 10 shared; set 3 FunFams 2 and 7 with 2
    shared
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule has fundamental logical errors (action deprecate), while condition sets 1, 3 and 4 are
    strongly supported and the term is correct for all four.
  correction: >-
    The stated reasons did not support the action and contradicted the summary. The action is kept
    for a different reason: the rule is withdrawn and the term obsolete.
  error_type: OTHER
  evidence:
  - 'rest.uniprot.org/arba/ARBA00047244: HTTP 404 on 2026-11-09'
  - 'QuickGO: GO:0043605 isObsolete = true'
- date: '2026-11-10'
  withdrawn_claim: GO:0043419 urea catabolic process is a more specific term for the urease set.
  correction: GO:0043419 is not an is_a descendant of GO:0043605.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - QuickGO is_a ancestors of GO:0043419 do not include GO:0043605
- date: '2026-11-10'
  withdrawn_claim: Literature support is strong, per deep-research summaries.
  correction: Generated research notes are not literature; the assessment is removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - Previous supported_by cited ARBA00047244-deep-research-perplexity.md and -falcon.md only