ARBA00028538 obsolete membrane lipid biosynthetic process (GO:0046467)

id: ARBA00028538
description: >-
  ARBA rule that assigned GO:0046467 membrane lipid biosynthetic process through 51 alternative condition
  sets built from InterPro, CATH FunFam and taxon conditions. GO has made the term obsolete and UniProt
  no longer serves the rule.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00028538
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR006634
      curie: InterPro:IPR006634
      label: TRAM/LAG1/CLN8 homology domain
      negated: false
    - condition_type: INTERPRO
      value: IPR016439
      curie: InterPro:IPR016439
      label: Sphingosine N-acyltransferase Lag1/Lac1-like
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR008901
      curie: InterPro:IPR008901
      label: Alkaline ceramidase
      negated: false
    - condition_type: TAXON
      value: Craniata
      curie: NCBITaxon:89593
      label: Craniata
      negated: false
    notes: >-
      Alkaline ceramidase family. Human ACER1 (Q8TDN7) has IPR008901 and is annotated to GO:0046512
      sphingosine biosynthetic process (IDA, PMID:17713573 and PMID:20628055) and GO:0030148 sphingolipid
      biosynthetic process (IDA, PMID:17713573).
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR001675
      curie: InterPro:IPR001675
      label: Glycosyl transferase family 29
      negated: false
    - condition_type: INTERPRO
      value: IPR051757
      curie: InterPro:IPR051757
      label: Beta-galactoside alpha2-3 sialyltransferases
      negated: false
    - condition_type: TAXON
      value: Euarchontoglires
      curie: NCBITaxon:314146
      label: Euarchontoglires
      negated: false
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR002347
      curie: InterPro:IPR002347
      label: Short-chain dehydrogenase/reductase SDR
      negated: false
    - condition_type: INTERPRO
      value: IPR020904
      curie: InterPro:IPR020904
      label: Short-chain dehydrogenase/reductase, conserved site
      negated: false
    - condition_type: INTERPRO
      value: IPR045022
      curie: InterPro:IPR045022
      label: 3-ketodihydrosphingosine reductase KDSR-like
      negated: false
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR004843
      curie: InterPro:IPR004843
      label: Calcineurin-like, phosphoesterase domain
      negated: false
    - condition_type: INTERPRO
      value: IPR008139
      curie: InterPro:IPR008139
      label: Saposin B type domain
      negated: false
    - condition_type: INTERPRO
      value: IPR045473
      curie: InterPro:IPR045473
      label: Sphingomyelin phosphodiesterase, C-terminal domain
      negated: false
    notes: >-
      Acid sphingomyelinase architecture. Human SMPD1 (P17405) has all three signatures and is annotated
      to GO:0046513 ceramide biosynthetic process (IDA, PMID:17303575, PMID:18815062, PMID:20807762,
      PMID:33163980; IMP, PMID:19279011, PMID:8706124).
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR007577
      curie: InterPro:IPR007577
      label: Glycosyltransferase, DXD sugar-binding motif
      negated: false
    - condition_type: INTERPRO
      value: IPR051706
      curie: InterPro:IPR051706
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
  - number: 7
    conditions:
    - condition_type: INTERPRO
      value: IPR004960
      curie: InterPro:IPR004960
      label: Bacterial lipid A biosynthesis acyltransferase
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 1.10.10.60:FF:000020
      curie: CATH.FunFam:1.10.10.60:FF:000020
      label: Ceramide synthase 5
      negated: false
    - condition_type: TAXON
      value: Metazoa
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.720:FF:000165
      curie: CATH.FunFam:3.40.50.720:FF:000165
      label: 3-ketodihydrosphingosine reductase
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 2.40.160.20:FF:000002
      curie: CATH.FunFam:2.40.160.20:FF:000002
      label: Lipid A palmitoyltransferase PagP
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.20:FF:000001
      curie: CATH.FunFam:3.90.550.20:FF:000001
      label: MIPC synthase subunit (SurA)
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000151
      curie: CATH.FunFam:1.10.510.10:FF:000151
      label: Serine/threonine-protein kinase
      negated: false
    - condition_type: FUNFAM
      value: 2.30.29.30:FF:000056
      curie: CATH.FunFam:2.30.29.30:FF:000056
      label: Serine/threonine-protein kinase
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      Human PRKD1 (Q15139) and PRKD2 (Q9BZL6) carry both FunFams and are annotated to GO:0030148 sphingolipid
      biosynthetic process as a Reactome traceable author statement (R-HSA-1660661).
  - number: 13
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000001
      curie: CATH.FunFam:3.40.50.2000:FF:000001
      label: UDP-glucuronosyltransferase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000033
      curie: CATH.FunFam:3.40.50.2000:FF:000033
      label: 2-hydroxyacylsphingosine 1-beta-galactosyltransferase
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
  - number: 14
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000069
      curie: CATH.FunFam:3.40.50.2000:FF:000069
      label: Alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000115
      curie: CATH.FunFam:3.40.50.2000:FF:000115
      label: Alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
      negated: false
    - condition_type: TAXON
      value: Bacillati
      curie: NCBITaxon:1783272
      label: Bacillati
      negated: false
  - number: 15
    conditions:
    - condition_type: FUNFAM
      value: 2.60.40.2300:FF:000001
      curie: CATH.FunFam:2.60.40.2300:FF:000001
      label: N-acylsphingosine amidohydrolase 2
      negated: false
    - condition_type: TAXON
      value: Mammalia
      curie: NCBITaxon:40674
      label: Mammalia
      negated: false
    notes: >-
      Human ASAH2 (Q9NR71) carries this FunFam and is annotated to GO:0046513 ceramide biosynthetic
      process (IDA, PMID:17475390; IMP, PMID:11278489) and GO:0046512 sphingosine biosynthetic process
      (IMP, PMID:30154232).
  - number: 16
    conditions:
    - condition_type: FUNFAM
      value: 3.10.120.10:FF:000011
      curie: CATH.FunFam:3.10.120.10:FF:000011
      label: Fatty acid 2-hydroxylase
      negated: false
    - condition_type: TAXON
      value: Craniata
      curie: NCBITaxon:89593
      label: Craniata
      negated: false
  - number: 17
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000111
      curie: CATH.FunFam:3.40.50.2000:FF:000111
      label: Monogalactosyldiacylglycerol synthase 3, chloroplastic
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
  - number: 18
    conditions:
    - condition_type: FUNFAM
      value: 3.40.640.10:FF:000049
      curie: CATH.FunFam:3.40.640.10:FF:000049
      label: serine palmitoyltransferase 1 isoform X1
      negated: false
    - condition_type: TAXON
      value: Vertebrata
      curie: NCBITaxon:7742
      label: Vertebrata
      negated: false
  - number: 19
    conditions:
    - condition_type: FUNFAM
      value: 3.60.21.10:FF:000045
      curie: CATH.FunFam:3.60.21.10:FF:000045
      label: Sphingomyelin phosphodiesterase
      negated: false
    - condition_type: TAXON
      value: Euteleostomi
      curie: NCBITaxon:117571
      label: Euteleostomi
      negated: false
    notes: Human SMPD1 (P17405) carries this FunFam; see set 5 for its annotations.
  - number: 20
    conditions:
    - condition_type: FUNFAM
      value: 3.90.1480.20:FF:000002
      curie: CATH.FunFam:3.90.1480.20:FF:000002
      label: CMP-N-acetylneuraminate-beta-galactosamide- alpha-2,3-sialyltransferase 2
      negated: false
    - condition_type: TAXON
      value: Eutheria
      curie: NCBITaxon:9347
      label: Eutheria
      negated: false
  - number: 21
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000037
      curie: CATH.FunFam:3.90.550.10:FF:000037
      label: Beta-1,4-galactosyltransferase 6
      negated: false
    - condition_type: TAXON
      value: Glires
      curie: NCBITaxon:314147
      label: Glires
      negated: false
  - number: 22
    conditions:
    - condition_type: FUNFAM
      value: 3.40.720.10:FF:000015
      curie: CATH.FunFam:3.40.720.10:FF:000015
      label: GPI ethanolamine phosphate transferase 1
      negated: false
  - number: 23
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000119
      curie: CATH.FunFam:3.90.550.10:FF:000119
      label: Dolichol-phosphate mannosyltransferase subunit 1
      negated: false
  - number: 24
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1700.10:FF:000001
      curie: CATH.FunFam:3.30.1700.10:FF:000001
      label: UDP-3-O-acyl-N-acetylglucosamine deacetylase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.230.20:FF:000001
      curie: CATH.FunFam:3.30.230.20:FF:000001
      label: UDP-3-O-acyl-N-acetylglucosamine deacetylase
      negated: false
    - condition_type: TAXON
      value: Pseudomonadati
      curie: NCBITaxon:3379134
      label: Pseudomonadati
      negated: false
  - number: 25
    conditions:
    - condition_type: FUNFAM
      value: 3.40.1090.10:FF:000014
      curie: CATH.FunFam:3.40.1090.10:FF:000014
      label: Patatin like phospholipase domain containing 1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.1090.10:FF:000016
      curie: CATH.FunFam:3.40.1090.10:FF:000016
      label: Patatin like phospholipase domain containing 1
      negated: false
    - condition_type: TAXON
      value: Euarchontoglires
      curie: NCBITaxon:314146
      label: Euarchontoglires
      negated: false
  - number: 26
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.1260:FF:000007
      curie: CATH.FunFam:3.40.50.1260:FF:000007
      label: Phosphoglycerate kinase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.1260:FF:000014
      curie: CATH.FunFam:3.40.50.1260:FF:000014
      label: Phosphoglycerate kinase
      negated: false
    - condition_type: TAXON
      value: Streptophyta
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: >-
      Arabidopsis chloroplast phosphoglycerate kinases PGKH1 (Q9LD57) and PGKH2 (P50318) carry both
      FunFams and are annotated to GO:0019375 galactolipid biosynthetic process (IGI, PMID:30834637).
  - number: 27
    conditions:
    - condition_type: FUNFAM
      value: 3.40.640.10:FF:000047
      curie: CATH.FunFam:3.40.640.10:FF:000047
      label: serine palmitoyltransferase 2 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 3.90.1150.10:FF:000004
      curie: CATH.FunFam:3.90.1150.10:FF:000004
      label: 2-amino-3-ketobutyrate coenzyme A ligase
      negated: false
    - condition_type: TAXON
      value: Hominidae
      curie: NCBITaxon:9604
      label: Hominidae
      negated: false
  - number: 28
    conditions:
    - condition_type: FUNFAM
      value: 1.20.144.10:FF:000034
      curie: CATH.FunFam:1.20.144.10:FF:000034
      label: Dihydrosphingosine-1-phosphate phosphatase
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
  - number: 29
    conditions:
    - condition_type: FUNFAM
      value: 1.20.144.10:FF:000044
      curie: CATH.FunFam:1.20.144.10:FF:000044
      label: Lipid A 1-phosphatase
      negated: false
    - condition_type: TAXON
      value: Campylobacterota
      curie: NCBITaxon:29547
      label: Campylobacterota
      negated: false
  - number: 30
    conditions:
    - condition_type: FUNFAM
      value: 3.10.120.10:FF:000021
      curie: CATH.FunFam:3.10.120.10:FF:000021
      label: Delta(8)-fatty-acid desaturase 2
      negated: false
    - condition_type: TAXON
      value: Embryophyta
      curie: NCBITaxon:3193
      label: Embryophyta
      negated: false
  - number: 31
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.10330:FF:000005
      curie: CATH.FunFam:3.40.50.10330:FF:000005
      label: Sphingosine kinase 2
      negated: false
    - condition_type: TAXON
      value: Homo
      curie: NCBITaxon:9605
      label: Homo
      negated: false
    notes: >-
      Human SPHK2 (Q9NRA0) carries this FunFam and is annotated to GO:0006669 sphinganine-1-phosphate
      biosynthetic process (IDA, PMID:10751414, PMID:19729656) and GO:0046512 sphingosine biosynthetic
      process (IGI and IMP, PMID:23106337).
  - number: 32
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000072
      curie: CATH.FunFam:3.40.50.2000:FF:000072
      label: Glycosyl transferase
      negated: false
    - condition_type: TAXON
      value: Mycobacteriales
      curie: NCBITaxon:85007
      label: Mycobacteriales
      negated: false
  - number: 33
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000145
      curie: CATH.FunFam:3.40.50.2000:FF:000145
      label: Probable glycosyl transferase
      negated: false
    - condition_type: TAXON
      value: Actinomycetota
      curie: NCBITaxon:201174
      label: Actinomycetota
      negated: false
  - number: 34
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.2000:FF:000207
      curie: CATH.FunFam:3.40.50.2000:FF:000207
      label: Phosphatidyl-myo-inositol mannosyltransferase
      negated: false
    - condition_type: TAXON
      value: Actinomycetes
      curie: NCBITaxon:1760
      label: Actinomycetes
      negated: false
  - number: 35
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.720:FF:000317
      curie: CATH.FunFam:3.40.50.720:FF:000317
      label: Very-long-chain 3-oxoacyl-CoA reductase
      negated: false
    - condition_type: TAXON
      value: Ascomycota
      curie: NCBITaxon:4890
      label: Ascomycota
      negated: false
  - number: 36
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.720:FF:000578
      curie: CATH.FunFam:3.40.50.720:FF:000578
      label: 3-ketodihydrosphingosine reductase
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
  - number: 37
    conditions:
    - condition_type: FUNFAM
      value: 3.40.640.10:FF:000006
      curie: CATH.FunFam:3.40.640.10:FF:000006
      label: 5-aminolevulinate synthase, mitochondrial
      negated: false
    - condition_type: TAXON
      value: Bacteroidota
      curie: NCBITaxon:976
      label: Bacteroidota
      negated: false
    notes: >-
      The two reviewed Bacteroidota members of this FunFam are serine palmitoyltransferases: Bacteroides
      thetaiotaomicron SPT (Q8A9E5) and Bacteroides ovatus SPT (A7LXM2). Of 1958 Bacteroidota members
      in UniProtKB, 52 are named serine palmitoyltransferase and none is named aminolevulinate synthase;
      many unreviewed ones are named 2-amino-3-ketobutyrate coenzyme A ligase.
  - number: 38
    conditions:
    - condition_type: FUNFAM
      value: 3.60.21.10:FF:000012
      curie: CATH.FunFam:3.60.21.10:FF:000012
      label: UDP-2,3-diacylglucosamine hydrolase
      negated: false
    - condition_type: TAXON
      value: Pseudomonadota
      curie: NCBITaxon:1224
      label: Pseudomonadota
      negated: false
  - number: 39
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000164
      curie: CATH.FunFam:3.90.550.10:FF:000164
      label: Beta-(1-3)-glucosyl transferase
      negated: false
    - condition_type: TAXON
      value: Cyanobacteriota
      curie: NCBITaxon:1117
      label: Cyanobacteriota
      negated: false
  - number: 40
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000207
      curie: CATH.FunFam:3.90.550.10:FF:000207
      label: Ceramide glucosyltransferase 1
      negated: false
    - condition_type: TAXON
      value: Ecdysozoa
      curie: NCBITaxon:1206794
      label: Ecdysozoa
      negated: false
  - number: 41
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000323
      curie: CATH.FunFam:3.90.550.10:FF:000323
      label: Processive diacylglycerol beta-glycosyltransferase
      negated: false
    - condition_type: TAXON
      value: Mycoplasmatota
      curie: NCBITaxon:544448
      label: Mycoplasmatota
      negated: false
  - number: 42
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.20:FF:000013
      curie: CATH.FunFam:3.90.550.20:FF:000013
      label: Alpha1,4-N-acetylgalactosaminyltransferase
      negated: false
    - condition_type: TAXON
      value: Arthropoda
      curie: NCBITaxon:6656
      label: Arthropoda
      negated: false
  - number: 43
    conditions:
    - condition_type: FUNFAM
      value: 3.90.76.10:FF:000006
      curie: CATH.FunFam:3.90.76.10:FF:000006
      label: Monoacyl phosphatidylinositol tetramannoside-binding protein
      negated: false
    - condition_type: TAXON
      value: Mycobacteriaceae
      curie: NCBITaxon:1762
      label: Mycobacteriaceae
      negated: false
  - number: 44
    conditions:
    - condition_type: FUNFAM
      value: 1.10.150.50:FF:000037
      curie: CATH.FunFam:1.10.150.50:FF:000037
      label: sphingomyelin synthase-related protein 1 isoform X1
      negated: false
  - number: 45
    conditions:
    - condition_type: FUNFAM
      value: 3.20.20.80:FF:000030
      curie: CATH.FunFam:3.20.20.80:FF:000030
      label: Lysosomal acid glucosylceramidase
      negated: false
    notes: >-
      Human GBA1 (P04062) carries this FunFam and is annotated to GO:0046513 ceramide biosynthetic
      process (IMP, PMID:19279011) and GO:0009247 glycolipid biosynthetic process (IDA, PMID:24211208,
      PMID:26724485).
  - number: 46
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.10320:FF:000002
      curie: CATH.FunFam:3.40.50.10320:FF:000002
      label: Probable N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
      negated: false
  - number: 47
    conditions:
    - condition_type: FUNFAM
      value: 3.40.720.10:FF:000041
      curie: CATH.FunFam:3.40.720.10:FF:000041
      label: GPI ethanolamine phosphate transferase 3
      negated: false
  - number: 48
    conditions:
    - condition_type: FUNFAM
      value: 3.60.21.10:FF:000022
      curie: CATH.FunFam:3.60.21.10:FF:000022
      label: Putative metallophosphoesterase 1
      negated: false
  - number: 49
    conditions:
    - condition_type: FUNFAM
      value: 3.90.1480.20:FF:000009
      curie: CATH.FunFam:3.90.1480.20:FF:000009
      label: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 isoform X2
      negated: false
  - number: 50
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.10:FF:000036
      curie: CATH.FunFam:3.90.550.10:FF:000036
      label: Dolichol-phosphate mannosyltransferase subunit 1
      negated: false
  - number: 51
    conditions:
    - condition_type: FUNFAM
      value: 3.90.550.50:FF:000019
      curie: CATH.FunFam:3.90.550.50:FF:000019
      label: Hexosyltransferase
      negated: false
  go_annotations:
  - go_id: GO:0046467
    go_label: obsolete membrane lipid biosynthetic process
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2025-12-15'
  retrieved_date: '2026-11-09'
  withdrawn: true
review_summary: >-
  GO:0046467 is obsolete in GO, and UniProt returned 404 for this rule on 2026-11-09. The 51 condition
  sets recorded are those of the last version reviewed. Nine of them (sets 2, 5, 12, 15, 19, 26, 31,
  37 and 45) were checked against Swiss-Prot members and their GO annotations. In each case a matched
  protein carries a curated annotation to a lipid biosynthetic process: the ceramidases, sphingomyelinase
  and glucosylceramidase are annotated to biosynthesis of their products ceramide and sphingosine;
  protein kinase D and the chloroplast phosphoglycerate kinases are annotated to sphingolipid and
  galactolipid biosynthesis; and the Bacteroidota set selects serine palmitoyltransferases. So these
  sets reflect existing annotations rather than fold-level errors. The other 42 sets were not checked.
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.'
- >-
  If rules for the same families are re-derived with current terms, do not exclude the hydrolase sets
  (2, 5, 15, 19, 45) on the ground that hydrolysis is catabolic: their Swiss-Prot members are experimentally
  annotated to ceramide or sphingosine biosynthetic process.
- >-
  For set 37, check the unreviewed Bacteroidota members named 2-amino-3-ketobutyrate coenzyme A ligase
  before propagating a sphingolipid term from the two reviewed serine palmitoyltransferases.
go_specificity:
  assessment: MISMATCHED
  notes: The consequent GO:0046467 is obsolete.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0046467
  label: obsolete membrane lipid biosynthetic process
  assessment: UNDECIDED
  consequent_obsolete: true
  correct_examples:
  - P17405
  - Q9NR71
  - Q8TDN7
  - P04062
  - Q9NRA0
  - Q8A9E5
  - Q9LD57
  - P50318
  - Q15139
  - Q9BZL6
  notes: >-
    QuickGO, 2026-11-09: GO:0046467 isObsolete = true, so the consequent itself cannot be assessed.
    The examples are reviewed proteins that match a checked condition set and carry a curated annotation
    under GO:0008610 lipid biosynthetic process: P17405 GO:0046513 IDA PMID:17303575; Q9NR71 GO:0046513
    IDA PMID:17475390; Q8TDN7 GO:0046512 IDA PMID:17713573; P04062 GO:0046513 IMP PMID:19279011; Q9NRA0
    GO:0006669 IDA PMID:10751414; Q9LD57 and P50318 GO:0019375 IGI PMID:30834637; Q15139 and Q9BZL6
    GO:0030148 TAS Reactome:R-HSA-1660661. Q8A9E5 is a reviewed serine palmitoyltransferase (EC 2.3.1.50).
confidence: 0.95
references:
- id: PMID:34445706
  title: >-
    Acid Sphingomyelinase, a Lysosomal and Secretory Phospholipase C, Is Key for Cellular Phospholipid
    Catabolism.
  findings:
  - statement: >-
      The paper states: "sphingolipids of mammalian cells are degraded in a stepwise manner without
      an effective bypass in human lysosomal catabolism"
  - statement: >-
      The paper states: "The recessively inherited ASMD mainly leads to impaired cellular SM catabolism
      causing progressive SM accumulation in the cellular membranes."
- id: PMID:38458396
  title: >-
    Common and varied molecular responses of Escherichia coli to five different inhibitors of the
    lipopolysaccharide biosynthetic enzyme LpxC.
  findings:
  - statement: >-
      The paper states: "The essential enzyme LpxC catalyzes the first committed step of LPS synthesis
      and thus represents a promising antibiotic target"
  - statement: >-
      The paper states: "Instead of the first enzyme LpxA, which catalyzes a reversible reaction,
      the second enzyme, LpxC, is the main driver in this process as it catalyzes the first committed
      step"
- id: PMID:26563290
  title: 'Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling.'
  findings:
  - statement: >-
      The paper states: "ethanolamine phosphate (EtNP), three mannoses (Mans), one non-N-acetylated
      glucosamine, and inositol phospholipid"
  - statement: >-
      The paper states: "Fatty chains of inositol phospholipids are inserted into the outer leaflet
      of the plasma membrane"
- id: PMID:26139634
  title: >-
    Functional classification of CATH superfamilies: a domain-based approach for protein function
    annotation.
  findings:
  - statement: >-
      The paper states: "the functional annotations provided by FunFams are found to be more precise
      compared with those generated by other domain-based resources"
- id: PMID:34357010
  title: Ceramide Metabolism Enzymes-Therapeutic Targets against Cancer.
  findings:
  - statement: 'The paper states: "ceramidases catalyze the degradation of ceramide to sphingosine"'
  - statement: >-
      The paper states: "alkaline ceramidases (encoded by ACER1, ACER2 and ACER3), acidic ceramidase
      (encoded by ASAH1) and neutral ceramidase (encoded by ASAH2)"
- id: PMID:28942130
  title: Biosynthesis and structure-activity relationships of the lipid A family of glycolipids.
  findings:
  - statement: >-
      The paper states: "Lipid A, the conserved, lipid component of LPS, anchors LPS to the outer
      membrane"
  - statement: >-
      The paper states: "E. coli acyl transferases are chain length specific, orthologs from other
      Gram-negative bacteria are more tolerant, yielding a heterogeneous Lipid A composition of the
      outer membrane."
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Five condition sets (alkaline ceramidase, acid sphingomyelinase, neutral ceramidase, sphingomyelin
    phosphodiesterase, lysosomal glucosylceramidase) are catabolic, so a lipid biosynthesis term on
    them would be false.
  correction: >-
    GO curators annotate these hydrolases to biosynthesis of their lipid products, with experimental
    evidence.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - 'QuickGO: P17405 (SMPD1) GO:0046513 ceramide biosynthetic process, IDA, PMID:17303575'
  - 'QuickGO: Q9NR71 (ASAH2) GO:0046513, IDA, PMID:17475390'
  - 'QuickGO: Q8TDN7 (ACER1) GO:0046512 sphingosine biosynthetic process, IDA, PMID:17713573'
  - 'QuickGO: P04062 (GBA1) GO:0046513, IMP, PMID:19279011'
- date: '2026-11-10'
  withdrawn_claim: >-
    Set 37 is 5-aminolevulinate synthase, a fold-level false positive that the Bacteroidota restriction
    conceals.
  correction: >-
    With the taxon condition applied, the reviewed members are serine palmitoyltransferases, the first
    enzyme of sphingolipid synthesis; the FunFam label alone was read.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    UniProtKB query xref funfam-3.40.640.10:FF:000006 AND taxonomy 976 AND reviewed: SPT_BACTN (Q8A9E5),
    SPT_BACO1 (A7LXM2)
  - >-
    Same query, all entries: 1958; with protein name aminolevulinate: 0; with protein name serine
    palmitoyltransferase: 52
- date: '2026-11-10'
  withdrawn_claim: Set 12 is a PH-domain protein kinase with no route to lipid biosynthesis.
  correction: >-
    The set matches protein kinase D1 and D2, which carry a curated sphingolipid biosynthesis annotation.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - 'QuickGO: Q15139 (PRKD1) and Q9BZL6 (PRKD2) GO:0030148, TAS, Reactome:R-HSA-1660661'
  - UniProtKB Q15139 and Q9BZL6 FunFams include 1.10.510.10:FF:000151 and 2.30.29.30:FF:000056
- date: '2026-11-10'
  withdrawn_claim: >-
    Set 26 is phosphoglycerate kinase, with no basis for a lipid biosynthetic annotation in Streptophyta
    or anywhere else.
  correction: >-
    The Arabidopsis chloroplast phosphoglycerate kinases matched by the set are annotated to galactolipid
    biosynthetic process from a genetic study.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - 'QuickGO: Q9LD57 (PGKH1) and P50318 (PGKH2) GO:0019375, IGI, PMID:30834637'
- date: '2026-11-10'
  withdrawn_claim: Set 31 (sphingosine kinase 2) is interconversion, not biosynthesis.
  correction: SPHK2 is experimentally annotated to biosynthetic process terms for sphingoid bases.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - >-
    QuickGO: Q9NRA0 GO:0006669 sphinganine-1-phosphate biosynthetic process, IDA, PMID:10751414
  - 'QuickGO: Q9NRA0 GO:0046512, IGI, PMID:23106337'
- date: '2026-11-10'
  withdrawn_claim: >-
    Four mechanistically unrelated sets reveal that the rule was built by following shared folds.
  correction: >-
    Three of the four (sets 12, 26 and 37) trace to curated annotations on the matched proteins; set
    43 was not checked.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - See the receipts for sets 12, 26 and 37 above
- date: '2026-11-10'
  withdrawn_claim: >-
    Per-set verdicts for the remaining sets (non-diagnostic, wrong pathway, annotation-bias taxon
    scopes) and the count of at most 26 sound sets.
  correction: >-
    These rested on reading FunFam and superfamily labels without checking matched proteins, the method
    that failed for the sets above; they are removed rather than kept unverified.
  error_type: UNEXAMINED_RULE
  evidence:
  - 42 of 51 condition sets were not checked against Swiss-Prot members
- date: '2026-11-10'
  withdrawn_claim: UniProt still serves the rule.
  correction: UniProt returned 404 on 2026-11-09.
  error_type: STALE_RULE_VERSION
  evidence:
  - 'rest.uniprot.org/arba/ARBA00028538: HTTP 404 on 2026-11-09'