ARBA00027389 cell wall biogenesis (GO:0042546)

id: ARBA00027389
description: Assigns GO:0042546 cell wall biogenesis through 34 alternative condition sets. Every set combines one
  to three InterPro, PANTHER or CATH FunFam conditions with a taxon condition; the taxa range from single fungal
  and plant clades to Bacteria and "not Vertebrata".
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00027389
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR025846
      curie: InterPro:IPR025846
      label: Trichome birefringence-like, N-terminal domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR026057
      curie: InterPro:IPR026057
      label: Trichome birefringence-like, C-terminal domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: Liliopsida
      curie: NCBITaxon:4447
      label: Liliopsida
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 14. 14 carry GO:0042546 or a descendant with evidence
      other than ARBA (14 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 5232.'
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR005150
      curie: InterPro:IPR005150
      label: Cellulose synthase
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR013083
      curie: InterPro:IPR013083
      label: Zinc finger, RING/FYVE/PHD-type
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR027934
      curie: InterPro:IPR027934
      label: Cellulose synthase, RING-type zinc finger
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 22. 19 carry GO:0042546 or a descendant with evidence
      other than ARBA (19 non-IEA, 0 other IEA); 3 carry it only from ARBA; 0 do not carry it. Not supported: A2XN66
      (CESA2 Probable cellulose synthase A catalytic subunit 2 [UDP-forming]); A2Y0X2 (CESA1 Probable cellulose
      synthase A catalytic subunit 1 [UDP-forming]); A2XNT2 (CESA5 Probable cellulose synthase A catalytic subunit
      5 [UDP-forming]). UniProtKB entries matching: 5573.'
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR009644
      curie: InterPro:IPR009644
      label: FKTN/Mannosyltransferase regulator
      interpro_type: FAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR15407:SF28
      curie: PANTHER:PTHR15407:SF28
      label: RIBITOL-5-PHOSPHATE TRANSFERASE FKTN
      negated: false
    - condition_type: TAXON
      value: Pichiomycetes
      curie: NCBITaxon:3239874
      label: Pichiomycetes
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 7. 6 carry GO:0042546 or a descendant with evidence
      other than ARBA (6 non-IEA, 0 other IEA); 0 carry it only from ARBA; 1 do not carry it. Not supported: A0A1D8PMM6
      (MNN4 Mannosyltransferase regulator 4). UniProtKB entries matching: 388.'
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR000873
      curie: InterPro:IPR000873
      label: AMP-dependent synthetase/ligase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR025110
      curie: InterPro:IPR025110
      label: AMP-binding enzyme, C-terminal domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR040097
      curie: InterPro:IPR040097
      label: Fatty acyl-AMP ligase /fatty acyl-CoA ligase
      interpro_type: FAMILY
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 26. 9 carry GO:0042546 or a descendant with evidence
      other than ARBA (9 non-IEA, 0 other IEA); 17 carry it only from ARBA; 0 do not carry it. Not supported: Q02278
      (fadD28 Long-chain-fatty-acid--AMP ligase FadD28); P9WQ42 (fadD26 Long-chain-fatty-acid--AMP ligase FadD26);
      P9WQ49 (fadD21 Putative fatty-acid--CoA ligase FadD21); C5BK10 (ttuA Medium-chain-fatty-acid--[acyl-carrier-protein]
      ligase TtuA); P9WQ58 (fadD28 Long-chain-fatty-acid--AMP ligase FadD28); Q6E7K9 (jamA Medium-chain-fatty-acid--[acyl-carrier-protein]
      ligase JamA); and others. UniProtKB entries matching: 5023.'
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR022751
      curie: InterPro:IPR022751
      label: Alpha-mannosyltransferase
      interpro_type: FAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR31646:SF1
      curie: PANTHER:PTHR31646:SF1
      label: ALPHA-1,2-MANNOSYLTRANSFERASE MNN2
      negated: false
    - condition_type: TAXON
      value: Debaryomycetaceae
      curie: NCBITaxon:766764
      label: Debaryomycetaceae
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 6. 6 carry GO:0042546 or a descendant with evidence
      other than ARBA (6 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 196.'
  - number: 6
    conditions:
    - condition_type: PANTHER
      value: PTHR13533
      curie: PANTHER:PTHR13533
      label: N-ACETYLNEURAMINATE 9-O-ACETYLTRANSFERASE
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 8. 7 carry GO:0042546 or a descendant with evidence
      other than ARBA (7 non-IEA, 0 other IEA); 0 carry it only from ARBA; 1 do not carry it. Not supported: F4K5L5
      (TBL16 Protein trichome birefringence-like 16). UniProtKB entries matching: 3140.'
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000009
      curie: CATH.FunFam:3.90.550.10:FF:000009
      label: Cellulose synthase
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 24. 21 carry GO:0042546 or a descendant with evidence
      other than ARBA (21 non-IEA, 0 other IEA); 3 carry it only from ARBA; 0 do not carry it. Not supported: A2XN66
      (CESA2 Probable cellulose synthase A catalytic subunit 2 [UDP-forming]); A2Y0X2 (CESA1 Probable cellulose
      synthase A catalytic subunit 1 [UDP-forming]); A2XNT2 (CESA5 Probable cellulose synthase A catalytic subunit
      5 [UDP-forming]). UniProtKB entries matching: 5917.'
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.12780:FF:000013
      curie: CATH.FunFam:3.40.50.12780:FF:000013
      label: Long-chain-fatty-acid--AMP ligase FadD32
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 30. 10 carry GO:0042546 or a descendant with evidence
      other than ARBA (10 non-IEA, 0 other IEA); 20 carry it only from ARBA; 0 do not carry it. Not supported: A0R618
      (fadD32 Long-chain-fatty-acid--AMP ligase FadD32); B2HMK0 (fadD32 Long-chain-fatty-acid--AMP ligase FadD32);
      Q02278 (fadD28 Long-chain-fatty-acid--AMP ligase FadD28); C5BK10 (ttuA Medium-chain-fatty-acid--[acyl-carrier-protein]
      ligase TtuA); P9WQ58 (fadD28 Long-chain-fatty-acid--AMP ligase FadD28); Q6E7K9 (jamA Medium-chain-fatty-acid--[acyl-carrier-protein]
      ligase JamA); and others. UniProtKB entries matching: 6958.'
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 2.40.440.10:FF:000001
      curie: CATH.FunFam:2.40.440.10:FF:000001
      label: L,D-transpeptidase YbiS
      negated: false
    - condition_type: TAXON
      value: Pseudomonadati
      curie: NCBITaxon:3379134
      label: Pseudomonadati
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 7. 7 carry GO:0042546 or a descendant with evidence
      other than ARBA (5 non-IEA, 2 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 1559.'
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1200.10:FF:000007
      curie: CATH.FunFam:1.10.1200.10:FF:000007
      label: Probable polyketide synthase pks17
      negated: false
    - condition_type: FUNFAM
      value: 3.30.300.30:FF:000042
      curie: CATH.FunFam:3.30.300.30:FF:000042
      label: Fatty-acid-CoA ligase FadD22
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.12780:FF:000055
      curie: CATH.FunFam:3.40.50.12780:FF:000055
      label: Fatty-acid-CoA ligase FadD22
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 4. 3 carry GO:0042546 or a descendant with evidence
      other than ARBA (3 non-IEA, 0 other IEA); 1 carry it only from ARBA; 0 do not carry it. Not supported: P9WQ60
      (fadD22 p-hydroxybenzoic acid--AMP ligase FadD22). UniProtKB entries matching: 11.'
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 2.160.10.10:FF:000017
      curie: CATH.FunFam:2.160.10.10:FF:000017
      label: Mannose-1-phosphate guanyltransferase
      negated: false
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000013
      curie: CATH.FunFam:3.90.550.10:FF:000013
      label: mannose-1-phosphate guanyltransferase beta
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 12. 1 carry GO:0042546 or a descendant with evidence
      other than ARBA (1 non-IEA, 0 other IEA); 1 carry it only from ARBA; 10 do not carry it. Not supported: P41940
      (PSA1 Mannose-1-phosphate guanyltransferase); O93827 (MPG1 Mannose-1-phosphate guanyltransferase); Q4I1Y5
      (MPG1 Mannose-1-phosphate guanyltransferase); Q6BN12 (MPG1 Mannose-1-phosphate guanyltransferase); Q9P8N0
      (MPG1 Mannose-1-phosphate guanyltransferase); O74484 (mpg1 Mannose-1-phosphate guanyltransferase); and others.
      UniProtKB entries matching: 1045.'
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000052
      curie: CATH.FunFam:3.40.50.2000:FF:000052
      label: Alpha-1,3-glucan synthase Ags2
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 4. 4 carry GO:0042546 or a descendant with evidence
      other than ARBA (4 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 1520.'
  - number: 13
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000096
      curie: CATH.FunFam:3.90.550.10:FF:000096
      label: Glycosyltransferases
      negated: false
    - condition_type: TAXON
      value: Streptophyta
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 3. 3 carry GO:0042546 or a descendant with evidence
      other than ARBA (3 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 740.'
  - number: 14
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1200.10:FF:000005
      curie: CATH.FunFam:1.10.1200.10:FF:000005
      label: Nonribosomal peptide synthetase 1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.47.10:FF:000042
      curie: CATH.FunFam:3.40.47.10:FF:000042
      label: Polyketide synthase Pks13
      negated: false
    - condition_type: TAXON
      value: Actinomycetota
      curie: NCBITaxon:201174
      label: Actinomycetota
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 3. 3 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 1 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 50.'
  - number: 15
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1200.10:FF:000019
      curie: CATH.FunFam:1.10.1200.10:FF:000019
      label: Phenolpthiocerol synthesis type-I polyketide synthase PPSA
      negated: false
    - condition_type: FUNFAM
      value: 1.10.1200.10:FF:000025
      curie: CATH.FunFam:1.10.1200.10:FF:000025
      label: Phenolpthiocerol synthesis polyketide synthase PpsA
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.250:FF:000003
      curie: CATH.FunFam:3.30.70.250:FF:000003
      label: Polyketide beta-ketoacyl synthase Pks3
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 3. 3 carry GO:0042546 or a descendant with evidence
      other than ARBA (3 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 5.'
  - number: 16
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000417
      curie: CATH.FunFam:1.10.510.10:FF:000417
      label: Leucine-rich repeat receptor-like protein kinase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.200.20:FF:000687
      curie: CATH.FunFam:3.30.200.20:FF:000687
      label: LRR receptor-like serine/threonine-protein kinase GSO1
      negated: false
    - condition_type: FUNFAM
      value: 3.80.10.10:FF:000101
      curie: CATH.FunFam:3.80.10.10:FF:000101
      label: LRR receptor-like serine/threonine-protein kinase ERECTA
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 306.'
  - number: 17
    conditions:
    - condition_type: FUNFAM
      value: 1.10.555.10:FF:000052
      curie: CATH.FunFam:1.10.555.10:FF:000052
      label: Rho GTPase-activating protein REN1
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000302
      curie: CATH.FunFam:2.30.29.30:FF:000302
      label: Rho GTPase-activating protein 7
      negated: false
    - condition_type: TAXON
      value: Embryophyta
      curie: NCBITaxon:3193
      label: Embryophyta
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 440.'
  - number: 18
    conditions:
    - condition_type: FUNFAM
      value: 3.10.129.110:FF:000003
      curie: CATH.FunFam:3.10.129.110:FF:000003
      label: Probable polyketide synthase pks1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.366.10:FF:000002
      curie: CATH.FunFam:3.40.366.10:FF:000002
      label: Probable polyketide synthase 2
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.11460:FF:000001
      curie: CATH.FunFam:3.40.50.11460:FF:000001
      label: Probable polyketide synthase pks1
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 6.'
  - number: 19
    conditions:
    - condition_type: FUNFAM
      value: 3.10.129.110:FF:000007
      curie: CATH.FunFam:3.10.129.110:FF:000007
      label: Phthiocerol synthesis polyketide synthase type I PpsC
      negated: false
    - condition_type: FUNFAM
      value: 3.40.47.10:FF:000019
      curie: CATH.FunFam:3.40.47.10:FF:000019
      label: Polyketide synthase type I
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.720:FF:000209
      curie: CATH.FunFam:3.40.50.720:FF:000209
      label: Polyketide synthase Pks12
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 5.'
  - number: 20
    conditions:
    - condition_type: FUNFAM
      value: 3.30.310.50:FF:000001
      curie: CATH.FunFam:3.30.310.50:FF:000001
      label: Phosphoglucosamine mutase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.120.10:FF:000001
      curie: CATH.FunFam:3.40.120.10:FF:000001
      label: Phosphoglucosamine mutase
      negated: false
    - condition_type: TAXON
      value: Pseudomonadota
      curie: NCBITaxon:1224
      label: Pseudomonadota
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 316. 71 carry GO:0042546 or a descendant with evidence
      other than ARBA (11 non-IEA, 60 other IEA); 245 carry it only from ARBA; 0 do not carry it. Not supported:
      A0Q8C5 (glmM Phosphoglucosamine mutase); A1KV99 (glmM Phosphoglucosamine mutase); A1U605 (glmM Phosphoglucosamine
      mutase); A1VQI3 (glmM Phosphoglucosamine mutase); A1WEE4 (glmM Phosphoglucosamine mutase); A3N856 (glmM Phosphoglucosamine
      mutase); and others. UniProtKB entries matching: 6456.'
  - number: 21
    conditions:
    - condition_type: FUNFAM
      value: 3.40.47.10:FF:000014
      curie: CATH.FunFam:3.40.47.10:FF:000014
      label: Chalcone synthase 1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.47.10:FF:000053
      curie: CATH.FunFam:3.40.47.10:FF:000053
      label: Alpha-pyrone synthesis polyketide synthase
      negated: false
    - condition_type: TAXON
      value: Actinomycetes
      curie: NCBITaxon:1760
      label: Actinomycetes
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 6. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 4 carry it only from ARBA; 0 do not carry it. Not supported: P9WPF4
      (pks10 Polyketide synthase-like Pks10); P9WPF2 (pks11 Methyl-branched alkylpyrone synthesis polyketide synthase-like
      Pks11); Q7VEU7 (pks11 Methyl-branched alkylpyrone synthesis polyketide synthase-like Pks11); Q7VEV2 (pks10
      Polyketide synthase-like Pks10). UniProtKB entries matching: 176.'
  - number: 22
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000040
      curie: CATH.FunFam:1.10.510.10:FF:000040
      label: Mitogen-activated protein kinase
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 4. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 2 carry it only from ARBA; 0 do not carry it. Not supported: P36005
      (KDX1 Serine/threonine-protein kinase KDX1); C4YGK0 (CEK1 Extracellular signal-regulated kinase 1). UniProtKB
      entries matching: 287.'
  - number: 23
    conditions:
    - condition_type: FUNFAM
      value: 1.50.10.20:FF:000006
      curie: CATH.FunFam:1.50.10.20:FF:000006
      label: Mannan endo-1,6-alpha-mannosidase
      negated: false
    - condition_type: TAXON
      value: Pichiomycetes
      curie: NCBITaxon:3239874
      label: Pichiomycetes
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 166.'
  - number: 24
    conditions:
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000405
      curie: CATH.FunFam:2.30.29.30:FF:000405
      label: RHO1 GDP-GTP exchange protein 2
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      curie: NCBITaxon:451866
      label: Taphrinomycotina
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 2.'
  - number: 25
    conditions:
    - condition_type: FUNFAM
      value: 2.60.40.150:FF:000170
      curie: CATH.FunFam:2.60.40.150:FF:000170
      label: Protein CELLULOSE SYNTHASE INTERACTIVE 1
      negated: false
    - condition_type: TAXON
      value: Tracheophyta
      curie: NCBITaxon:58023
      label: Tracheophyta
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 602.'
  - number: 26
    conditions:
    - condition_type: FUNFAM
      value: 3.20.20.370:FF:000008
      curie: CATH.FunFam:3.20.20.370:FF:000008
      label: Chitin deacetylase
      negated: false
    - condition_type: TAXON
      value: Saccharomycetes
      curie: NCBITaxon:4891
      label: Saccharomycetes
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 60.'
  - number: 27
    conditions:
    - condition_type: FUNFAM
      value: 3.20.20.70:FF:000254
      curie: CATH.FunFam:3.20.20.70:FF:000254
      label: 2-dehydro-3-deoxyphosphooctonate aldolase 2
      negated: false
    - condition_type: TAXON
      value: Spermatophyta
      curie: NCBITaxon:58024
      label: Spermatophyta
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 47.'
  - number: 28
    conditions:
    - condition_type: FUNFAM
      value: 3.20.20.80:FF:000038
      curie: CATH.FunFam:3.20.20.80:FF:000038
      label: 1,3-beta-glucanosyltransferase
      negated: false
    - condition_type: TAXON
      value: Schizosaccharomycetes
      curie: NCBITaxon:147554
      label: Schizosaccharomycetes
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 7.'
  - number: 29
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.150:FF:000350
      curie: CATH.FunFam:3.40.50.150:FF:000350
      label: Probable pectin methylesterase CGR3
      negated: false
    - condition_type: TAXON
      value: Magnoliopsida
      curie: NCBITaxon:3398
      label: Magnoliopsida
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 52.'
  - number: 30
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000535
      curie: CATH.FunFam:3.40.50.300:FF:000535
      label: rac-like GTP-binding protein RAC2
      negated: false
    - condition_type: TAXON
      value: Malvales
      curie: NCBITaxon:41938
      label: Malvales
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 119.'
  - number: 31
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000648
      curie: CATH.FunFam:3.40.50.300:FF:000648
      label: Stage IV sporulation protein A
      negated: false
    - condition_type: TAXON
      value: Bacillota
      curie: NCBITaxon:1239
      label: Bacillota
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 2. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 793.'
  - number: 32
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.60:FF:000002
      curie: CATH.FunFam:3.90.550.60:FF:000002
      label: Galactofuranosyl transferase GlfT1
      negated: false
    - condition_type: TAXON
      value: Mycobacteriaceae
      curie: NCBITaxon:1762
      label: Mycobacteriaceae
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 3. 2 carry GO:0042546 or a descendant with evidence
      other than ARBA (2 non-IEA, 0 other IEA); 1 carry it only from ARBA; 0 do not carry it. Not supported: P9WMX2
      (glfT1 Galactofuranosyltransferase GlfT1). UniProtKB entries matching: 44.'
  - number: 33
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.720:FF:000046
      curie: CATH.FunFam:3.40.50.720:FF:000046
      label: UDP-N-acetylmuramate--L-alanine ligase
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 144. 144 carry GO:0042546 or a descendant with evidence
      other than ARBA (7 non-IEA, 137 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 1878.'
  - number: 34
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000084
      curie: CATH.FunFam:3.90.550.10:FF:000084
      label: Glycosyltransferases
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: true
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 3. 3 carry GO:0042546 or a descendant with evidence
      other than ARBA (3 non-IEA, 0 other IEA); 0 carry it only from ARBA; 0 do not carry it. UniProtKB entries
      matching: 524.'
  go_annotations:
  - go_id: GO:0042546
    go_label: cell wall biogenesis
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 34
review_summary: 'All 34 live condition sets were queried against Swiss-Prot, counting a match as supported when
  it carries GO:0042546 or a descendant with evidence other than ARBA. In 22 sets every reviewed match is supported;
  in 12 sets (CS2, CS3, CS4, CS6, CS7, CS8, CS10, CS11, CS20, CS21, CS22, CS32) only some are; no set is without
  support. The partly supported sets include mycobacterial cell-envelope lipid enzymes whose curated terms are descendants
  of GO:0042546, such as FadD26 P9WQ43 and PpsA P9WQE7 with GO:0071770 by IDA from PMID:15749014, and two sets where
  support is thin: CS11 (fungal mannose-1-phosphate guanylyltransferases, 1 of 12 supported) and CS20 (phosphoglucosamine
  mutase GlmM in Pseudomonadota, 71 of 316). An unsupported match is one without curated annotation, not one shown
  to be wrong, so these counts do not settle whether CS11 and CS20 are sound.'
action: UNDECIDED
action_rationale: Most sets are supported by curated annotation and no false positive was identified, but for CS11
  and CS20 most reviewed matches lack any independent annotation to the term, and that question was not resolved.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0042546
  label: cell wall biogenesis
  assessment: UNDECIDED
  correct_examples:
  - P9WQ43
  - P9WQE7
  - P96202
  - Q4U3E8
  notes: 'P9WQ43 (M. tuberculosis fadD26): GO:0071766 IDA PMID:20553505; GO:0071770 IDA PMID:15749014 and IMP PMID:11279114
    (MTBBASE). P9WQE7 (ppsA) and P96202: GO:0071770 IDA PMID:15749014. Q4U3E8 (A. fumigatus mpg1): GO:0070590 IMP
    PMID:18757806. GO:0071770 DIM/DIP cell wall layer assembly and GO:0071766 Actinobacterium-type cell wall biogenesis
    are descendants of GO:0042546 in QuickGO by is_a/part_of. QuickGO lists 1271 annotations attributed to ARBA:ARBA00027389
    (2026-11-10).'
corrections:
- date: '2026-11-10'
  withdrawn_claim: Polyketide synthases and fatty acid ligases in the rule have no direct role in cell wall synthesis.
  correction: The polyketide synthase and fatty-acyl-AMP ligase sets are restricted to Actinomycetota, Actinomycetes,
    Mycobacteriaceae or Bacteria, where these enzymes build cell-envelope lipids and carry experimental cell wall
    biogenesis annotations.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - 'UniProtKB P9WQE7 (ppsA, M. tuberculosis): GO:0071770 DIM/DIP cell wall layer assembly, IDA PMID:15749014 (MTBBASE)'
  - 'UniProtKB P9WQ43 (fadD26): GO:0071766 IDA PMID:20553505; GO:0071770 IDA PMID:15749014'
  - 'QuickGO: GO:0071770 has GO:0042546 among its is_a/part_of ancestors'
  - 'Live CS14 (FunFams 1.10.1200.10:FF:000005 AND 3.40.47.10:FF:000042 AND Actinomycetota): 3 Swiss-Prot matches,
    all PpsE (Q7TXL6, P9WQE1, P9WQE0), all supported'
- date: '2026-11-10'
  withdrawn_claim: Only 7 of 29 condition sets target genuine cell wall enzymes; the other 22 target unrelated proteins.
  correction: The earlier file recorded no condition sets, so this count had no basis. The live rule has 34 sets
    and each has at least one reviewed match with independent annotation to the term or a descendant.
  error_type: UNEXAMINED_RULE
  evidence:
  - 'Live rule: 34 condition sets (2026-11-09)'
  - 'Swiss-Prot support per set recorded in rule.condition_sets notes: 22 fully supported, 12 partly, 0 unsupported'
- date: '2026-11-10'
  withdrawn_claim: Protein families such as receptor kinases, Rho GTPase regulators and polyketide synthases were
    judged unrelated to the cell wall from their family names.
  correction: Each family appears only together with a taxon condition and, mostly, further signature conditions;
    the families cannot be judged without them.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Live rule: all 34 sets carry a taxon condition'
  - 'CS16 (three FunFams, not Vertebrata): 2 Swiss-Prot matches, both supported; CS17 (two FunFams, Embryophyta):
    2 matches, both supported'
- date: '2026-11-10'
  withdrawn_claim: 'Literature contradicts the annotations (literature_support: CONTRADICTED), and the review quotes
    a file ARBA00027389.enriched.json.'
  correction: No publication was cited for the contradiction, and the quoted file is not in the rule folder.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - rules/arba/ARBA00027389/ contains no ARBA00027389.enriched.json
- date: '2026-11-10'
  withdrawn_claim: The rule spans 21 taxonomic groups, and this breadth increases false positive risk.
  correction: The taxa are per-set restrictions that narrow each set. The number of different taxa used across sets
    is not a measure of risk.
  error_type: TAXON_MISREAD
  evidence:
  - 'Live rule: every one of 34 sets has a taxon condition'