source: candidates: projects/RAR_MISANNOTATION/data/rar_rerun_direct_candidates.yaml scope: kingdom-level candidates flagged in Plants or Animals triage_date: '2026-11-11' status: FIRST_PASS method: Five groups (plant IBA, plant inferred, plant experimental, animal inferred, animal experimental), each triaged against GO term definitions and constraints (QuickGO), protein identity and curated function (UniProt), the PAINT node or mapping behind each row, and cached papers where quoted; then merged with a coverage check and a check that every proposed replacement id is a live GO term. verdicts: 'ANNOTATION_WRONG, CONSTRAINT_QUESTIONABLE, FLAG_FAILS, TRUE_BUT_GENERAL, UNCERTAIN as in rar_rerun_triage.yaml, plus DEFER_TO_CURATOR: an experimental row whose term can apply to the lineage, with the full text not read. Experimental rows are not overruled on first-pass evidence; they are called ANNOTATION_WRONG only when the term''s definition or GO taxon constraint excludes the lineage, as a term choice.' note: First-pass verdicts; nothing is filed upstream. Verbatim quotes are given where a cached paper or UniProt record decides the verdict; other reasons rest on QuickGO and UniProt REST lookups and PubMed abstracts. totals: terms: 958 entries: 987 verdicts: ANNOTATION_WRONG: 139 CONSTRAINT_QUESTIONABLE: 4 DEFER_TO_CURATOR: 379 FLAG_FAILS: 363 TRUE_BUT_GENERAL: 36 UNCERTAIN: 66 groups: - group: plants_iba terms: 128 entry_count: 129 verdicts: ANNOTATION_WRONG: 18 CONSTRAINT_QUESTIONABLE: 1 FLAG_FAILS: 96 UNCERTAIN: 14 summary: '128 terms, 129 entries (GO:0044038 split by species). Verdicts: FLAG_FAILS 96, ANNOTATION_WRONG 18, UNCERTAIN 14, CONSTRAINT_QUESTIONABLE 1. Most flags are curation-density artefacts: plant metabolic enzymes (purine, arginine, thiamine, biotin, histidine) where bacteria dominate the denominator, and conserved eukaryotic machinery (replication, repair, splicing, cohesin, Pol I) that is simply under-curated in plants. The ANNOTATION_WRONG calls are all over-deep PAINT nodes carrying animal-only biology onto plant proteins: TNF/TNFR, Wnt, NOS-dependent NO regulation (DDAH), heparan sulfate, S100 calcium-dependent binding, BORC lysosome positioning, GATOR2/SEACAT (SEH1, SEC13), ESCRT-0, myosin II/myosin filament, polytene chromosome, centrosome, astral microtubules, FASTK RNA granules and ALAS (land plants use the C5 pathway). Selaginella''s flagellate sperm make the cilium/IFT/transition-zone rows consistent, and the Metazoa-only constraint on sperm axoneme assembly looks too narrow.' fetched_pmids: [] entries: - go_id: GO:0005813 label: centrosome aspect: CC annotations: - UniProtKB:D8RR71 (Selaginella, IBA) - UniProtKB:Q9M2Q7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000471210 verdict: ANNOTATION_WRONG reason: G-patch proteins (At3g57910, D8RR71) inherit centrosome from a node seeded only by human GPATCH11 (Q8N954); land plants have no centrosomes and the rows break GO's never_in_taxon Viridiplantae constraint. - go_id: GO:0008933 label: peptidoglycan lytic transglycosylase activity aspect: MF annotations: - UniProtKB:D8SPF8 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002410022 verdict: UNCERTAIN reason: D8SPF8 is in PANTHER subfamily PTHR30163:SF8 (lytic murein transglycosylase) under an E. coli/Pseudomonas-seeded node. The activity needs a peptidoglycan substrate; settle by showing plastid peptidoglycan in Selaginella (it has MurA and MraY homologs, as mosses with plastid PG do). - go_id: GO:0045041 label: protein import into mitochondrial intermembrane space aspect: BP annotations: - UniProtKB:Q8GYJ4 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000492699; other: InterPro:IPR039289' verdict: FLAG_FAILS reason: Arabidopsis MIA40 (IPR039289) is the IMS import receptor; the plant mitochondrial disulfide-relay pathway is real and only one plant protein is annotated. - go_id: GO:0030695 label: GTPase regulator activity aspect: MF annotations: - UniProtKB:D8T2B9 (Selaginella, IBA) mechanism: IBA PANTHER:PTN004747825 verdict: FLAG_FAILS reason: D8T2B9 is in PANTHER subfamily PTHR31010:SF2 (Ran-specific GAP 30, yeast YRB30 seed); the Ran GTPase cycle exists in plants. The low rate reflects a rarely-used general term. - go_id: GO:1990228 label: sulfurtransferase complex aspect: CC annotations: - UniProtKB:Q9FXE3 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000978101 verdict: FLAG_FAILS reason: Arabidopsis SUFE2 activates plastid cysteine desulfurase NFS2 (UniProt FUNCTION, PubMed:17452319), the plant counterpart of the E. coli CsdA-CsdE pair that seeds the node. - go_id: GO:0097163 label: sulfur carrier activity aspect: MF annotations: - UniProtKB:Q9FXE3 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000978101 verdict: FLAG_FAILS reason: SUFE2 accepts persulfide sulfur from NFS2 for Fe-S assembly, a SufE-family property; plant rarity is curation density. - go_id: GO:0009009 label: site-specific recombinase activity aspect: MF annotations: - UniProtKB:D8RBV8 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001251457 verdict: UNCERTAIN reason: D8RBV8 (1401 aa, tyrosine-recombinase domain, current PANTHER PTHR21446:SF12) sits under a node seeded only by E. coli XerC/XerD. A eukaryotic protein inside a bacterial Xer clade suggests a transposon-encoded recombinase or a contaminating contig; settle by checking whether D8RBV8 is a DIRS/Crypton-type transposon ORF and what other eukaryotes the node holds. - go_id: GO:0005246 label: calcium channel regulator activity aspect: MF annotations: - UniProtKB:D8RUD1 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN001031746; other: InterPro:IPR037608' verdict: UNCERTAIN reason: The node is seeded by STIM1/STIM2. D8RUD1 matches the STIM1/2 InterPro entry (IPR037608) and PANTHER STIM family (PTHR15136), but its only Pfam domain is SAM; Selaginella also has Orai-domain proteins (Pfam PF07856, e.g. D8RGM9). Settle by checking D8RUD1 for the TM and SOAR/CAD regions needed to gate Orai; if present, a lycophyte SOCE pair is rare real biology. - go_id: GO:0008157 label: protein phosphatase 1 binding aspect: MF annotations: - UniProtKB:Q8S8F7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000464544 verdict: FLAG_FAILS reason: INH3 is a PP1 regulatory/inhibitory subunit; PP1 binding is its defining property and plant PP1 regulators are simply under-curated. - go_id: GO:1904262 label: negative regulation of TORC1 signaling aspect: BP annotations: - UniProtKB:D8S7M9 (Selaginella, IBA) - UniProtKB:D8T401 (Selaginella, IBA) - UniProtKB:Q9M391 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000366325 verdict: UNCERTAIN reason: Ataxin-3 homologs (At3g54130, two Selaginella Josephin proteins) inherit this from a node seeded only by human ATXN3 (P54252). Plant TOR signalling exists but lacks TSC/Rheb and Rag-GATOR modules; settle by identifying the TORC1 input ATXN3 acts on in human and whether plants have it. - go_id: GO:0006363 label: termination of RNA polymerase I transcription aspect: BP annotations: - UniProtKB:D8R331 (Selaginella, IBA) - UniProtKB:D8SMF0 (Selaginella, IBA) - UniProtKB:Q9LU97 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000133053 verdict: FLAG_FAILS reason: RPA12-family Pol I subunits; Rpa12-mediated Pol I termination is a conserved eukaryotic process and plants have Pol I. - go_id: GO:0065002 label: intracellular protein transmembrane transport aspect: BP annotations: - UniProtKB:D8RAV0 (Selaginella, IBA) - UniProtKB:D8RH88 (Selaginella, IBA) - UniProtKB:Q9SJV5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000769484 verdict: FLAG_FAILS reason: TatC (chloroplast Tat translocase) moves folded proteins across the thylakoid membrane; correct for Arabidopsis TATC and its Selaginella orthologs. - go_id: GO:0031293 label: membrane protein intracellular domain proteolysis aspect: BP annotations: - UniProtKB:F4JUU5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN004417004 verdict: FLAG_FAILS reason: Arabidopsis S2P is the site-2 protease that releases the cytosolic domains of membrane-bound bZIP17/bZIP28; regulated intramembrane proteolysis exists in plants. - go_id: GO:0034023 label: 5-(carboxyamino)imidazole ribonucleotide mutase activity aspect: MF annotations: - UniProtKB:Q9SJ42 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000549177 verdict: FLAG_FAILS reason: At2g05140 is a PurE-type CAIR mutase fragment; plants use the bacterial-type PurK/PurE route, so the activity is right and the low rate reflects that animals use PAICS instead. - go_id: GO:0035869 label: ciliary transition zone aspect: CC annotations: - UniProtKB:D8QTL3 (Selaginella, IBA) - UniProtKB:D8SBR2 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000401088 verdict: FLAG_FAILS reason: Selaginella has flagellate sperm; D8QTL3/D8SBR2 are KAP3 (kinesin-2 associated protein) homologs from a node seeded by mouse Kifap3. GO's constraint excludes only seed plants, so the Selaginella rows are consistent. - go_id: GO:0044689 label: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase activity aspect: MF annotations: - UniProtKB:D8RBF3 (Selaginella, IBA/IEA) - UniProtKB:D8RY80 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN000540995; other: EC:4.3.1.32' verdict: FLAG_FAILS reason: D8RBF3/D8RY80 are CofH/CofG FO synthases (EC 4.3.1.32 mapping agrees). FO (photolyase antenna chromophore) synthesis is rare in eukaryotes but domain architecture supports the activity; rare biology, possibly horizontally acquired. - go_id: GO:0030892 label: mitotic cohesin complex aspect: CC annotations: - UniProtKB:Q56YN8 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000434523 verdict: FLAG_FAILS reason: Arabidopsis SMC3 is the cohesin SMC subunit used in plant mitosis; correct, curation density only. - go_id: GO:1904263 label: positive regulation of TORC1 signaling aspect: BP annotations: - UniProtKB:D8RPE9 (Selaginella, IBA) - UniProtKB:D8SM57 (Selaginella, IBA) - UniProtKB:Q93VR9 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000111887 verdict: ANNOTATION_WRONG reason: SEH1/SEC13 act in TORC1 signalling only as GATOR2/SEACAT members. Arabidopsis, Selaginella and Physcomitrella have no NPRL2 (PTHR12991), WDR24 (PTHR46200) or MIOS (PTHR16453) family members in UniProt, so plant SEH1/SEC13 are nucleoporins and COPII coat proteins only. The node is placed above a lineage that lost the SEA/GATOR complexes. - go_id: GO:0000107 label: imidazoleglycerol-phosphate synthase activity aspect: MF annotations: - UniProtKB:D8RBX3 (Selaginella, IBA/IEA) - UniProtKB:D8RXQ1 (Selaginella, IBA/IEA) - UniProtKB:Q9SZ30 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000477998; other: InterPro:IPR004651, InterPro:IPR014640, RHEA:24793' verdict: FLAG_FAILS reason: HISN4 is the bifunctional glutaminase/cyclase IGP synthase of plant histidine biosynthesis (UniProt FUNCTION); animals lack the pathway, hence the low plant rate. - go_id: GO:0071030 label: nuclear mRNA surveillance of spliceosomal pre-mRNA splicing aspect: BP annotations: - UniProtKB:O23676 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000290902 verdict: FLAG_FAILS reason: MAGO (EJC core) row comes from a node seeded by one S. pombe experiment (mnh1); nuclear surveillance of mis-spliced pre-mRNA is a general eukaryotic process with nothing animal-specific. - go_id: GO:0140597 label: protein carrier activity aspect: MF annotations: - UniProtKB:D8RF76 (Selaginella, IBA) - UniProtKB:D8SDD1 (Selaginella, IBA) - UniProtKB:Q6GKV1 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000305707 verdict: FLAG_FAILS reason: GET4 is a conserved GET-pathway component that hands tail-anchored proteins to GET3; the GET pathway is characterised in Arabidopsis. - go_id: GO:0000346 label: transcription export complex aspect: CC annotations: - UniProtKB:Q8L4M1 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN002547886 verdict: FLAG_FAILS reason: THO6 is a TREX/THO subunit; the TREX complex exists in plants. - go_id: GO:0001002 label: RNA polymerase III type 1 promoter sequence-specific DNA binding aspect: MF annotations: - UniProtKB:F4HP69 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN001430930 verdict: FLAG_FAILS reason: F4HP69 is a TFIIIC subunit homolog (node seeded by yeast TFC6/tau91); plant 5S rRNA genes use type 1 Pol III promoters, so the concept applies. - go_id: GO:1903457 label: lactate catabolic process aspect: BP annotations: - UniProtKB:Q94AX4 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000202298 verdict: FLAG_FAILS reason: Arabidopsis D-LDH is the mitochondrial D-lactate dehydrogenase of methylglyoxal detoxification; lactate catabolism is correct. - go_id: GO:0034087 label: establishment of mitotic sister chromatid cohesion aspect: BP annotations: - UniProtKB:A5HEI1 (Arabidopsis, IBA) - UniProtKB:D8RFB7 (Selaginella, IBA) - UniProtKB:D8SDH0 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000496017 verdict: FLAG_FAILS reason: SCC2/Nipped-B cohesin loaders; establishment of cohesion is conserved and Arabidopsis SCC2 is characterised. - go_id: GO:0033209 label: tumor necrosis factor-mediated signaling pathway aspect: BP annotations: - UniProtKB:D8R5K7 (Selaginella, IBA) - UniProtKB:D8SFE0 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002313819 verdict: ANNOTATION_WRONG reason: D8SFE0/D8R5K7 are COMMD proteins (PTHR16231:SF4) inheriting from a node seeded only by human COMMD7. Plants have no TNF or TNF receptors (no PTHR11471 or PTHR46861 members in Arabidopsis or Selaginella). - go_id: GO:0032418 label: lysosome localization aspect: BP annotations: - UniProtKB:F4J1T2 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000337884 verdict: ANNOTATION_WRONG reason: KXD1 inherits this from human KXD1 (BORC). The BORC-specific subunits BORCS5, BORCS6, BORCS7 and BORCS8 have no PANTHER family members in Arabidopsis, and plants have lytic vacuoles rather than motile lysosomes; plant KXD1 can only act through BLOC-1. - go_id: GO:0043291 label: RAVE complex aspect: CC annotations: - UniProtKB:F4IJ68 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000359150 verdict: FLAG_FAILS reason: F4IJ68 is the Arabidopsis Rav1/DMXL homolog (node seeded by yeast and pombe Rav1); RAVE-type V-ATPase assembly regulation is plausibly eukaryote-wide. - go_id: GO:0048306 label: calcium-dependent protein binding aspect: MF annotations: - UniProtKB:D8RL71 (Selaginella, IBA) - UniProtKB:Q9XIR0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN007521306 verdict: ANNOTATION_WRONG reason: The node is seeded only by vertebrate S100 proteins (S100B, S100A6, S100P, S100A11). The plant proteins are in PANTHER PTHR37754 (calcium ion-binding protein), and the S100 family PTHR11639 has no members in Arabidopsis or Selaginella, so the node joins unrelated EF-hand clades. - go_id: GO:0000729 label: DNA double-strand break processing aspect: BP annotations: - UniProtKB:D8QPA7 (Selaginella, IBA) - UniProtKB:D8SL68 (Selaginella, IBA) - UniProtKB:Q9ZUL5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000743674 verdict: FLAG_FAILS reason: CHR19/ETL1 is the plant Fun30/SMARCAD1 remodeler, which promotes end resection in yeast and human; DSB processing exists in plants. - go_id: GO:0070914 label: UV-damage excision repair aspect: BP annotations: - UniProtKB:D8RQ83 (Selaginella, IBA) - UniProtKB:D8TDH1 (Selaginella, IBA) - UniProtKB:Q9MA98 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000297520 verdict: FLAG_FAILS reason: ERCC1 is the NER endonuclease subunit; Arabidopsis ERCC1 is characterised in UV repair. - go_id: GO:0051880 label: G-quadruplex DNA binding aspect: MF annotations: - UniProtKB:D8QZS8 (Selaginella, IBA) - UniProtKB:D8TC60 (Selaginella, IBA) - UniProtKB:Q9SL02 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000429848 verdict: FLAG_FAILS reason: RAD50 node; G-quadruplex DNA is not lineage-specific and nothing in the claim excludes plants. - go_id: GO:0052837 label: thiazole biosynthetic process aspect: BP annotations: - UniProtKB:D8RPN5 (Selaginella, IBA/IEA) - UniProtKB:D8TFQ8 (Selaginella, IBA/IEA) - UniProtKB:Q38814 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000065314; other: UniRule:UR000375967' verdict: FLAG_FAILS reason: THI1/THI4 thiazole synthase; correct, plants and fungi make thiamine and animals do not. - go_id: GO:0180020 label: membrane bending activity aspect: MF annotations: - UniProtKB:D8S6Z2 (Selaginella, IBA) - UniProtKB:D8T7G1 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001398562 verdict: FLAG_FAILS reason: PER33/POM33 (TMEM33 family) ER-shaping proteins; tubular ER exists in plants and the family is conserved. - go_id: GO:0005700 label: polytene chromosome aspect: CC annotations: - UniProtKB:D8RAW7 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002920257 verdict: ANNOTATION_WRONG reason: No polytene chromosomes are described in Selaginella, and nothing places D8RAW7 in one; the function arose in the Drosophila Set8 lineage below PTN002920257. (Polyteny itself occurs outside Diptera, e.g. in some plant suspensors, so the call rests on this protein, not on the term.) - go_id: GO:0051598 label: meiotic recombination checkpoint signaling aspect: BP annotations: - UniProtKB:F4HRV8 (Arabidopsis, IBA) - UniProtKB:Q8H1F9 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000554401, PANTHER:PTN008491432 verdict: UNCERTAIN reason: ASY1 and PCH2 sit under HORMAD1/HOP1 and PCH2 nodes. Arabidopsis PCH2 remodels the meiotic axis and matures crossovers (UniProt FUNCTION, PubMed:26182244), but no recombination checkpoint arrest is shown in plants. Settle with evidence that plant asy1/pch2 or recombination mutants trigger a meiotic checkpoint arrest. - go_id: GO:0006617 label: SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition aspect: BP annotations: - UniProtKB:D8T2Q1 (Selaginella, IBA) - UniProtKB:Q943Z6 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000425879 verdict: FLAG_FAILS reason: SRP19 is a core SRP subunit; cotranslational targeting is universal. - go_id: GO:0000403 label: Y-form DNA binding aspect: MF annotations: - UniProtKB:A0A1I9LR82 (Arabidopsis, IBA) - UniProtKB:D8SVF6 (Selaginella, IBA) - UniProtKB:D8T0Q4 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000325249 verdict: FLAG_FAILS reason: CSM3 (Tipin/Swi3) replication-fork protection; Y-form DNA binding is a conserved fork-protection property. - go_id: GO:0033176 label: proton-transporting V-type ATPase complex aspect: CC annotations: - UniProtKB:D8SKE5 (Selaginella, IBA) - UniProtKB:D8T0F9 (Selaginella, IBA) - UniProtKB:Q9XGM1 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN002268884 verdict: FLAG_FAILS reason: V-ATPase subunit D; plant V-ATPase is well characterised. - go_id: GO:0170057 label: RNA ligase (GTP) activity aspect: MF annotations: - UniProtKB:D8SNU5 (Selaginella, IBA/IEA) - UniProtKB:D8SS91 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN000122119; other: EC:6.5.1.8, InterPro:IPR001233, InterPro:IPR036025' verdict: FLAG_FAILS reason: D8SNU5/D8SS91 carry the RtcB domain (IPR001233; EC 6.5.1.8 mapping agrees); RtcB-type ligase in a lycophyte is rare but genuine domain-supported biology. - go_id: GO:0000707 label: meiotic DNA recombinase assembly aspect: BP annotations: - UniProtKB:Q8GXF0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000534385 verdict: FLAG_FAILS reason: Arabidopsis RAD51C is required for meiotic recombination; correct. - go_id: GO:0071162 label: CMG complex aspect: CC annotations: - UniProtKB:A0A1P8AW53 (Arabidopsis, IBA) - UniProtKB:D8R606 (Selaginella, IBA) - UniProtKB:D8SG75 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000308454 verdict: FLAG_FAILS reason: PSF1 is a GINS subunit of the CMG helicase; universal in eukaryotes. - go_id: GO:0030177 label: positive regulation of Wnt signaling pathway aspect: BP annotations: - UniProtKB:D8T779 (Selaginella, IBA) - UniProtKB:D8TE34 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000370137 verdict: ANNOTATION_WRONG reason: Cereblon homologs inherit this from human CRBN and Drosophila ohgata. Plants have no Wnt ligands (no PTHR12027 members in Arabidopsis or Selaginella) and no canonical Wnt pathway. - go_id: GO:0000730 label: DNA recombinase assembly aspect: BP annotations: - UniProtKB:D8R902 (Selaginella, IBA) - UniProtKB:P94102 (Arabidopsis, IBA) - UniProtKB:Q39009 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN001415033 verdict: FLAG_FAILS reason: RAD51, DMC1 and a RecA-domain paralog form recombinase filaments; universal in eukaryotes. - go_id: GO:0070987 label: error-free translesion synthesis aspect: BP annotations: - UniProtKB:A3EWL3 (Arabidopsis, IBA) - UniProtKB:D8R5R1 (Selaginella, IBA) - UniProtKB:D8SFY4 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000117973 verdict: FLAG_FAILS reason: REV1 and Pol eta are Y-family translesion polymerases; conserved in plants. - go_id: GO:0004076 label: biotin synthase activity aspect: MF annotations: - UniProtKB:D8QXQ4 (Selaginella, IBA/IEA) - UniProtKB:D8SDT9 (Selaginella, IBA/IEA) - UniProtKB:P54967 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000540961; other: EC:2.8.1.6, InterPro:IPR024177, RHEA:22060' verdict: FLAG_FAILS reason: BIO2 biotin synthase; plants make biotin, animals do not. EC/RHEA mappings agree. - go_id: GO:0008902 label: hydroxymethylpyrimidine kinase activity aspect: MF annotations: - UniProtKB:D8T631 (Selaginella, IBA/IEA) - UniProtKB:D8T7X1 (Selaginella, IBA/IEA) - UniProtKB:Q5M731 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000466159; other: EC:2.7.1.49, RHEA:23096' verdict: FLAG_FAILS reason: TH1 is the bifunctional HMP/HMP-P kinase of plant thiamine synthesis (UniProt family); correct. - go_id: GO:0008972 label: phosphomethylpyrimidine kinase activity aspect: MF annotations: - UniProtKB:D8T631 (Selaginella, IBA/IEA) - UniProtKB:D8T7X1 (Selaginella, IBA/IEA) - UniProtKB:Q5M731 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000466159; other: InterPro:IPR004399' verdict: FLAG_FAILS reason: 'As GO:0008902: TH1 second kinase step; correct.' - go_id: GO:0000444 label: MIS12/MIND type complex aspect: CC annotations: - UniProtKB:F4JT58 (Arabidopsis, IEA) - UniProtKB:Q2V0Z5 (Arabidopsis, IBA/ISS) mechanism: 'IBA PANTHER:PTN001427121; other: InterPro:IPR007128, UniProtKB:Q9H081' verdict: FLAG_FAILS reason: MIS12 and a PMF1/Nnf1 homolog (EMB3006) are MIS12-complex kinetochore subunits; the complex is conserved in plants. - go_id: GO:0042719 label: mitochondrial intermembrane space chaperone complex aspect: CC annotations: - UniProtKB:D8QP64 (Selaginella, IBA) - UniProtKB:Q9XGX9 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN004407763 verdict: FLAG_FAILS reason: TIM9 small Tim chaperone; conserved in plant mitochondria. - go_id: GO:0010833 label: telomere maintenance via telomere lengthening aspect: BP annotations: - UniProtKB:D0EL35 (Arabidopsis, IBA) - UniProtKB:D8QYM5 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001804660 verdict: FLAG_FAILS reason: CTC1 (CST complex) is characterised in Arabidopsis telomere maintenance. - go_id: GO:1990809 label: endoplasmic reticulum tubular network membrane organization aspect: BP annotations: - UniProtKB:D8S6Z2 (Selaginella, IBA) - UniProtKB:D8T7G1 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001398562 verdict: FLAG_FAILS reason: PER33/POM33 family, same node as GO:0180020; tubular ER exists in plants. - go_id: GO:0042799 label: histone H4K20 methyltransferase activity aspect: MF annotations: - UniProtKB:D8RAW7 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002920257 verdict: UNCERTAIN reason: D8RAW7 is in PANTHER PTHR48442, separate from the SET8/KMT5A family PTHR46167, yet inherits H4K20 methyltransferase from a node seeded only by Drosophila Set8. Plants carry H4K20me1 but no writer is known; settle with an H4 methylation assay or a current tree placing D8RAW7 with SET8. - go_id: GO:0036158 label: outer dynein arm assembly aspect: BP annotations: - UniProtKB:D8RLI1 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002925607 verdict: UNCERTAIN reason: D8RLI1 is a DNAAF4 family member (PTHR46492), and Selaginella has motile sperm, so the term is not excluded by lineage. But no Selaginella protein falls in the DNAH5 family (PTHR46532), which Chlamydomonas has (3), suggesting lycophyte axonemes may lack outer-arm dynein. Settle by establishing whether Selaginella sperm have outer dynein arms. - go_id: GO:0097020 label: COPII receptor activity aspect: MF annotations: - UniProtKB:D8RTD3 (Selaginella, IBA/IEA) - UniProtKB:D8SQS8 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN000321972; other: InterPro:IPR007277' verdict: FLAG_FAILS reason: SVP26/Erv26 is a COPII cargo receptor; conserved. - go_id: GO:0034067 label: protein localization to Golgi apparatus aspect: BP annotations: - UniProtKB:D8QTY2 (Selaginella, IBA) - UniProtKB:D8RJP1 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000196303 verdict: FLAG_FAILS reason: ARFRP1 recruits ARL1 to the TGN; plant ARFRP1 is conserved and the process exists. - go_id: GO:0140469 label: GCN2-mediated signaling aspect: BP annotations: - UniProtKB:D8T3H7 (Selaginella, IBA) - UniProtKB:D8TA44 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000418656 verdict: FLAG_FAILS reason: IMPACT/Yih1 homologs bind GCN1 to restrain GCN2; plants have GCN2 and GCN1, so the pathway exists (the role is negative regulation, but the row's broad term is consistent). - go_id: GO:0035770 label: ribonucleoprotein granule aspect: CC annotations: - UniProtKB:Q8VZE7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000477113 verdict: ANNOTATION_WRONG reason: Arabidopsis RAP is a chloroplast stroma/nucleoid 16S rRNA processing factor (UniProt, PubMed:24585838). The term comes from a node seeded by FASTK and FASTKD2/FASTKD5, animal stress-granule and mitochondrial RNA-granule proteins; nothing places plant RAP in an RNA granule. - go_id: GO:0035859 label: Seh1-associated complex aspect: CC annotations: - UniProtKB:D8RPE9 (Selaginella, IBA) - UniProtKB:D8SM57 (Selaginella, IBA) - UniProtKB:Q93VR9 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000111887 verdict: ANNOTATION_WRONG reason: 'Same problem as GO:1904263: the SEA complex needs Npr2/Npr3/Iml1 and Mtc5/Rtc1/Sea4 equivalents, none of which have PANTHER family members in Arabidopsis, Selaginella or Physcomitrella. Plant SEH1/SEC13 are nucleoporins/COPII subunits.' - go_id: GO:0007079 label: mitotic chromosome movement towards spindle pole aspect: BP annotations: - UniProtKB:F4ICA0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000649974 verdict: UNCERTAIN reason: KIN-8A is in subfamily PTHR47968:SF13 (KIF19-like) and inherits from a node seeded by yeast Kip3 and pombe Klp5/Klp6. Plants have anaphase A, so the process exists, but no mitotic role for plant kinesin-8 is shown; settle with a plant kin8 mitotic phenotype. - go_id: GO:0180022 label: RQC-trigger complex aspect: CC annotations: - UniProtKB:Q9SN77 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN008344380; other: InterPro:IPR009349' verdict: FLAG_FAILS reason: Q9SN77 carries the TRIP4/ASC-1 zinc finger (IPR009349); ribosome-associated quality control triggering is conserved. - go_id: GO:0032982 label: myosin filament aspect: CC annotations: - UniProtKB:D8R9M6 (Selaginella, IBA) mechanism: IBA PANTHER:PTN005210253 verdict: ANNOTATION_WRONG reason: Plants have no myosin II and no myosin filaments. D8R9M6 is a SKICH-domain protein (PTHR31915) annotated from a node seeded by animal and Dictyostelium myosin II light/heavy-chain genes. - go_id: GO:0061673 label: mitotic spindle astral microtubule aspect: CC annotations: - UniProtKB:F4ICA0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000649974 verdict: ANNOTATION_WRONG reason: Land-plant mitotic spindles are acentrosomal and have no astral microtubules; the KIN-8A row inherits this from yeast/pombe kinesin-8 seeds. - go_id: GO:0003847 label: 1-alkyl-2-acetylglycerophosphocholine esterase activity aspect: MF annotations: - UniProtKB:D8QS42 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN000031087; other: EC:3.1.1.47' verdict: FLAG_FAILS reason: D8QS42 is a PAF-AH II family member (PF03403); the node includes an S. pombe seed, so the esterase activity is placed at an ancient eukaryotic node. Rare but plausible biochemistry. - go_id: GO:0004536 label: DNA nuclease activity aspect: MF annotations: - UniProtKB:D8R4M4 (Selaginella, IBA) - UniProtKB:Q9LX74 (Arabidopsis, IEA) mechanism: 'IBA PANTHER:PTN002131615; other: RAP2022-09-01:Os03t0854200-01, UniProtKB:Q84T68' verdict: FLAG_FAILS reason: D8R4M4 sits under an Endonuclease I (E. coli endA, Vibrio Dns) node; RRP46 row is an IEA projection from rice OsRRP46. Nuclease biochemistry is not lineage-restricted. - go_id: GO:0032263 label: GMP salvage aspect: BP annotations: - UniProtKB:D8T0J1 (Selaginella, IBA) - UniProtKB:F4IA25 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000501530 verdict: FLAG_FAILS reason: HGPRT purine salvage; conserved. - go_id: GO:0004644 label: phosphoribosylglycinamide formyltransferase activity aspect: MF annotations: - UniProtKB:D8R2R3 (Selaginella, IBA/IEA) - UniProtKB:D8STB5 (Selaginella, IBA/IEA) - UniProtKB:P52422 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000055290; other: EC:2.1.2.2, InterPro:IPR004607, RHEA:15053' verdict: FLAG_FAILS reason: PUR3 GART; purine biosynthesis, EC/RHEA mappings agree. - go_id: GO:0004585 label: ornithine carbamoyltransferase activity aspect: MF annotations: - UniProtKB:D8SUH0 (Selaginella, IBA/IEA) - UniProtKB:D8SZY7 (Selaginella, IBA/IEA) - UniProtKB:O50039 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000150424; other: ARBA:ARBA00033579, EC:2.1.3.3, InterPro:IPR024904, RHEA:19513' verdict: FLAG_FAILS reason: Plastid OTC; arginine biosynthesis, correct. - go_id: GO:0004056 label: argininosuccinate lyase activity aspect: MF annotations: - UniProtKB:D8RTQ6 (Selaginella, IBA/IEA) - UniProtKB:D8T5F5 (Selaginella, IBA/IEA) - UniProtKB:Q9LEU8 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000154674; other: EC:4.3.2.1, InterPro:IPR009049, RHEA:24020' verdict: FLAG_FAILS reason: Argininosuccinate lyase; correct. - go_id: GO:0004087 label: carbamoyl-phosphate synthase (ammonia) activity aspect: MF annotations: - UniProtKB:D8RF71 (Selaginella, IBA/IEA) - UniProtKB:D8SDC5 (Selaginella, IBA/IEA) - UniProtKB:Q42601 (Arabidopsis, IBA/IEA/ISS) mechanism: 'IBA PANTHER:PTN008517424; other: EC:6.3.4.16, RHEA:18029, UniProtKB:P03965' verdict: FLAG_FAILS reason: Arabidopsis CARB lists both the glutamine-dependent and the NH4+-dependent reactions for the large chain (UniProt CATALYTIC ACTIVITY, PubMed:21265888); the large subunit does catalyse the ammonia reaction. - go_id: GO:0004360 label: L-glutamine:D-fructose-6-phosphate transaminase (isomerizing) activity aspect: MF annotations: - UniProtKB:D8STI3 (Selaginella, IBA/IEA) - UniProtKB:D8T582 (Selaginella, IBA/IEA) - UniProtKB:Q9LIP9 (Arabidopsis, IBA/IEA/ISS) mechanism: 'IBA PANTHER:PTN000101302; other: EC:2.6.1.16, InterPro:IPR005855, UniProtKB:P82808' verdict: FLAG_FAILS reason: GFAT; conserved hexosamine pathway enzyme. - go_id: GO:0019240 label: L-citrulline biosynthetic process aspect: BP annotations: - UniProtKB:D8SUH0 (Selaginella, IBA) - UniProtKB:D8SZY7 (Selaginella, IBA) - UniProtKB:O50039 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000150424 verdict: FLAG_FAILS reason: OTC makes citrulline in plastid arginine synthesis; correct. - go_id: GO:0004019 label: adenylosuccinate synthase activity aspect: MF annotations: - UniProtKB:D8RGZ6 (Selaginella, IBA/IEA) - UniProtKB:D8S5K6 (Selaginella, IBA/IEA) - UniProtKB:Q96529 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000217844; other: EC:6.3.4.4, InterPro:IPR001114, RHEA:15753, UniRule:UR000375791' verdict: FLAG_FAILS reason: PURA adenylosuccinate synthetase; correct. - go_id: GO:0004151 label: dihydroorotase activity aspect: MF annotations: - UniProtKB:D8R5M0 (Selaginella, IBA/IEA) - UniProtKB:D8SFC7 (Selaginella, IBA/IEA) - UniProtKB:O04904 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000791117; other: EC:3.5.2.3, InterPro:IPR004721, RHEA:24296' verdict: FLAG_FAILS reason: PYR4 dihydroorotase; correct. - go_id: GO:0160107 label: tRNA (adenine(58)-N1)-methyltransferase activity aspect: MF annotations: - UniProtKB:D8QU12 (Selaginella, IBA/IEA) - UniProtKB:D8QV77 (Selaginella, IBA/IEA) - UniProtKB:F4K6U9 (Arabidopsis, IEA) mechanism: 'IBA PANTHER:PTN000253097; other: EC:2.1.1.220, InterPro:IPR014816, RHEA:43152, UniRule:UR000415089' verdict: FLAG_FAILS reason: TRM61 tRNA m1A58 methyltransferase; conserved. - go_id: GO:0004639 label: phosphoribosylaminoimidazolesuccinocarboxamide synthase activity aspect: MF annotations: - UniProtKB:D8R9C8 (Selaginella, IBA/IEA) - UniProtKB:D8TAJ7 (Selaginella, IBA/IEA) - UniProtKB:P38025 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000176702; other: EC:6.3.2.6, InterPro:IPR018236, RHEA:22628' verdict: FLAG_FAILS reason: PUR7 SAICAR synthetase; correct. - go_id: GO:0017178 label: diphthine-ammonia ligase activity aspect: MF annotations: - UniProtKB:D8T289 (Selaginella, IBA/IEA) - UniProtKB:D8T858 (Selaginella, IBA/IEA) - UniProtKB:F4J3Q1 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000257633; other: EC:6.3.1.14' verdict: FLAG_FAILS reason: Diphthamide synthase DPH6; plants make diphthamide on eEF2. - go_id: GO:0046040 label: IMP metabolic process aspect: BP annotations: - UniProtKB:D8RGZ6 (Selaginella, IBA) - UniProtKB:D8S5K6 (Selaginella, IBA) - UniProtKB:Q96529 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000217844 verdict: FLAG_FAILS reason: Adenylosuccinate synthetase acts in IMP metabolism; correct. - go_id: GO:0008614 label: pyridoxine metabolic process aspect: BP annotations: - UniProtKB:D8QSM3 (Selaginella, IBA) - UniProtKB:D8R1U4 (Selaginella, IBA) - UniProtKB:Q8LAD0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000774355 verdict: FLAG_FAILS reason: PDX2 glutaminase subunit of the PDX1/PDX2 PLP synthase (UniProt FUNCTION); vitamin B6 metabolism is right. - go_id: GO:1903600 label: glutaminase complex aspect: CC annotations: - UniProtKB:D8QSM3 (Selaginella, IBA) - UniProtKB:D8R1U4 (Selaginella, IBA) - UniProtKB:Q8LAD0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000774355 verdict: FLAG_FAILS reason: The PDX1/PDX2 complex is the glutaminase complex of PLP synthesis; correct. - go_id: GO:0045429 label: positive regulation of nitric oxide biosynthetic process aspect: BP annotations: - UniProtKB:D8QPQ2 (Selaginella, IBA) - UniProtKB:D8SKS3 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000978164 verdict: ANNOTATION_WRONG reason: DDAH promotes NO synthesis by removing ADMA, an inhibitor of NO synthase. Land plants have no NOS (no PTHR43410 members in Arabidopsis or Selaginella), so the mechanism the node encodes (seeded by bovine/mouse/rat DDAH1/2) does not exist. - go_id: GO:0016242 label: negative regulation of macroautophagy aspect: BP annotations: - UniProtKB:D8RPQ3 (Selaginella, IBA) - UniProtKB:D8TFM6 (Selaginella, IBA) - UniProtKB:Q9FR53 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000124327 verdict: FLAG_FAILS reason: TOR represses autophagy in plants as in other eukaryotes; correct. - go_id: GO:0140567 label: membrane protein dislocase activity aspect: MF annotations: - UniProtKB:D8T896 (Selaginella, IBA) - UniProtKB:D8TBK6 (Selaginella, IBA) - UniProtKB:Q9LT02 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000643319 verdict: FLAG_FAILS reason: PDR2 is the plant P5A-ATPase; P5A ATPases (Spf1/ATP13A1) dislocate mistargeted tail-anchored proteins and the family is conserved. - go_id: GO:0007288 label: sperm axoneme assembly aspect: BP annotations: - UniProtKB:D8STG0 (Selaginella, IBA) - UniProtKB:D8T5A3 (Selaginella, IBA) mechanism: IBA PANTHER:PTN008557012 verdict: CONSTRAINT_QUESTIONABLE reason: Selaginella has motile biflagellate sperm, and CFAP43 is an axonemal protein conserved in flagellates. The only_in_taxon Metazoa constraint is too narrow for sperm axoneme assembly in lycophytes and ferns. - go_id: GO:0097681 label: double-strand break repair via alternative nonhomologous end joining aspect: BP annotations: - UniProtKB:D8T5V4 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000340766 verdict: UNCERTAIN reason: HMCES-family (SRAP) protein; alt-EJ involvement rests on human work and the mechanism in plants is untested. Settle with a plant hmces mutant phenotype in end joining. - go_id: GO:0140431 label: DNA-(abasic site) binding aspect: MF annotations: - UniProtKB:D8T5V4 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000340766 verdict: FLAG_FAILS reason: SRAP/HMCES domain proteins crosslink to abasic sites as a conserved family property across bacteria and eukaryotes. - go_id: GO:0031990 label: mRNA export from nucleus in response to heat stress aspect: BP annotations: - UniProtKB:D8SF75 (Selaginella, IBA) - UniProtKB:D8SRT7 (Selaginella, IBA) - UniProtKB:Q9C811 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000479965 verdict: FLAG_FAILS reason: NUP160 is required for mRNA export in Arabidopsis; heat-stress export is a conserved nucleoporin function. - go_id: GO:0015012 label: heparan sulfate proteoglycan biosynthetic process aspect: BP annotations: - UniProtKB:D8RMB9 (Selaginella, IBA) - UniProtKB:D8SLF0 (Selaginella, IBA) - UniProtKB:Q3EDG5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000301790 verdict: ANNOTATION_WRONG reason: Plants make no heparan sulfate. Arabidopsis TPST is a protein-tyrosine sulfotransferase (UniProt FUNCTION, PubMed:19666544), and the node is seeded by animal heparan sulfate sulfotransferases; plant EXT-family homologs are xylan/xyloglucan glycosyltransferases. - go_id: GO:0071018 label: U12-type catalytic step 2 spliceosome aspect: CC annotations: - UniProtKB:F4IGS5 (Arabidopsis, IBA) - UniProtKB:F4K2V9 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000468991 verdict: FLAG_FAILS reason: RBM48 is a minor-spliceosome component; plants have U12-type introns. - go_id: GO:0061504 label: cyclic threonylcarbamoyladenosine biosynthetic process aspect: BP annotations: - UniProtKB:D8QP30 (Selaginella, IBA) - UniProtKB:D8SIZ6 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001333297 verdict: FLAG_FAILS reason: TcdA-type ThiF-family dehydratases make cyclic t6A; ct6A occurs outside animals, so plant presence is plausible and rare in annotation. - go_id: GO:0051864 label: histone H3K36 demethylase activity aspect: MF annotations: - UniProtKB:D8QZ95 (Selaginella, IBA) - UniProtKB:D8R9X2 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000318179 verdict: UNCERTAIN reason: ROX family (NO66/MINA53) proteins; the node is seeded only by mouse Riox1. The main ROX activity is ribosomal histidyl hydroxylation and the H3K36 demethylase claim is not established for plant members; settle with a histone demethylation assay for the Selaginella proteins. - go_id: GO:0032210 label: regulation of telomere maintenance via telomerase aspect: BP annotations: - UniProtKB:Q56Y52 (Arabidopsis, IBA) - UniProtKB:Q6NKX5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000376531 verdict: FLAG_FAILS reason: POT1a/POT1b regulate telomerase in Arabidopsis (POT1b negatively, UniProt FUNCTION); the regulation term covers both. - go_id: GO:0003870 label: 5-aminolevulinate synthase activity aspect: MF annotations: - UniProtKB:D8R4V5 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000343737 verdict: ANNOTATION_WRONG reason: Land plants make 5-aminolevulinate by the C5 glutamyl-tRNA pathway, not ALAS. D8R4V5 falls in PANTHER subfamily PTHR13693:SF102 (2-amino-3-ketobutyrate CoA ligase) of the class II aminotransferase family, under an ALAS-seeded node. replacement: GO:0008890 glycine C-acetyltransferase activity (candidate, from subfamily; unassayed) - go_id: GO:0006208 label: pyrimidine nucleobase catabolic process aspect: BP annotations: - UniProtKB:D8R305 (Selaginella, IBA/IEA) - UniProtKB:D8SMH7 (Selaginella, IBA/IEA) - UniProtKB:Q9FMP3 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000182450; other: ARBA:ARBA00086398' verdict: FLAG_FAILS reason: PYD2 dihydropyrimidinase; plant pyrimidine catabolism is characterised. - go_id: GO:0002933 label: lipid hydroxylation aspect: BP annotations: - UniProtKB:Q9LNJ4 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN005383291 verdict: FLAG_FAILS reason: CYP703A2 in-chain hydroxylates lauric acid for sporopollenin (UniProt FUNCTION, PubMed:17496121); correct. - go_id: GO:0035720 label: intraciliary anterograde transport aspect: BP annotations: - UniProtKB:D8T911 (Selaginella, IBA) - UniProtKB:D8TD01 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000381369 verdict: FLAG_FAILS reason: IFT56 in Selaginella, which has flagellate sperm; GO's constraint excludes only seed plants. - go_id: GO:0031113 label: regulation of microtubule polymerization aspect: BP annotations: - UniProtKB:Q96262 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN008673654 verdict: FLAG_FAILS reason: PCAP1/MDP25 binds and destabilises cortical microtubules in a Ca2+-dependent way (UniProt FUNCTION); regulation of MT polymerization is correct. - go_id: GO:0016460 label: myosin II complex aspect: CC annotations: - UniProtKB:D8R3G0 (Selaginella, IBA) - UniProtKB:D8R9M6 (Selaginella, IBA) - UniProtKB:D8SI49 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000549249, PANTHER:PTN005210253 verdict: ANNOTATION_WRONG reason: Plants have no class II myosin. D8R3G0 is in subfamily PTHR23048:SF32 (dynein regulatory complex protein 8), D8SI49 is an EF-hand protein, and D8R9M6 is a SKICH-domain protein; all three inherit from myosin II light/heavy-chain nodes. - go_id: GO:0000417 label: HIR complex aspect: CC annotations: - UniProtKB:D8RWR3 (Selaginella, IBA) - UniProtKB:D8S688 (Selaginella, IBA) - UniProtKB:Q9LXN4 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000352669 verdict: FLAG_FAILS reason: HIRA is the plant H3.3 chaperone; HIR complex conserved. - go_id: GO:0120330 label: rixosome complex aspect: CC annotations: - UniProtKB:D8RTJ1 (Selaginella, IBA) - UniProtKB:D8SQZ5 (Selaginella, IBA) - UniProtKB:Q9M3B4 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000428096 verdict: FLAG_FAILS reason: RID3 is a WDR18/Ipi3-type rixosome subunit; conserved ribosome biogenesis complex. - go_id: GO:0009450 label: GABA catabolic process aspect: BP annotations: - UniProtKB:D8QTT0 (Selaginella, IBA/IEA) - UniProtKB:D8RJV5 (Selaginella, IBA/IEA) - UniProtKB:Q9SAK4 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN008681047; other: InterPro:IPR010102, UniProtKB-UniPathway:UPA00733, UniRule:UR001051784' verdict: FLAG_FAILS reason: ALDH5F1 SSADH; plant GABA shunt is characterised. - go_id: GO:0044038 label: cell wall macromolecule biosynthetic process aspect: BP annotations: - UniProtKB:O49730 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000531998 verdict: ANNOTATION_WRONG reason: Arabidopsis has no plastid peptidoglycan; its MraY homolog TRANS11 is described only as possibly involved in glycosylation (UniProt FUNCTION) and makes none of the polysaccharide wall. The term arrives from a node seeded by bacterial MraY (E. coli, Thermotoga). - go_id: GO:0044038 label: cell wall macromolecule biosynthetic process aspect: BP annotations: - UniProtKB:D8SF52 (Selaginella, IBA) - UniProtKB:D8SRQ9 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000531998 verdict: UNCERTAIN reason: 'Selaginella MraY homologs: right only if lycophyte plastids make peptidoglycan, as moss plastids do. Settle by detecting plastid peptidoglycan in Selaginella.' - go_id: GO:0071821 label: FANCM-MHF complex aspect: CC annotations: - UniProtKB:Q8L7N3 (Arabidopsis, IBA) - UniProtKB:Q9FI55 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000541279, PANTHER:PTN002010747; other: InterPro:IPR029003' verdict: FLAG_FAILS reason: MHF1/MHF2 work with FANCM in Arabidopsis; correct. - go_id: GO:0042758 label: long-chain fatty acid catabolic process aspect: BP annotations: - UniProtKB:D8QSL3 (Selaginella, IBA) - UniProtKB:D8R1T3 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001659973 verdict: UNCERTAIN reason: D8QSL3/D8R1T3 are AIG1-family (PTHR10989, PF04750) proteins fused to a RING domain, inheriting from human ADTRP/AIG1 (FAHFA hydrolases). The plant proteins are untested and FAHFA hydrolysis is not clearly long-chain fatty acid catabolism; settle with an activity assay. - go_id: GO:0005164 label: tumor necrosis factor receptor binding aspect: MF annotations: - UniProtKB:D8S6Y7 (Selaginella, IBA) - UniProtKB:D8SSY4 (Selaginella, IBA) - UniProtKB:D8T7F6 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002379609 verdict: ANNOTATION_WRONG reason: D8S6Y7/D8SSY4/D8T7F6 are B-box proteins classed with TRIM37 (PTHR36754), inheriting from a node seeded only by human TRIM37. Plants have no TNF receptors (no PTHR46861 members). - go_id: GO:0110155 label: NAD-cap decapping aspect: BP annotations: - UniProtKB:D8T6F9 (Selaginella, IBA) - UniProtKB:D8T6M0 (Selaginella, IBA) - UniProtKB:Q8RY73 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000273640 verdict: FLAG_FAILS reason: Arabidopsis DXO1 is a characterised deNADding enzyme; correct. - go_id: GO:0000454 label: snoRNA guided rRNA pseudouridine synthesis aspect: BP annotations: - UniProtKB:D8R5G8 (Selaginella, IBA) - UniProtKB:Q8VZT0 (Arabidopsis, IBA) - UniProtKB:Q9FK53 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000579935 verdict: FLAG_FAILS reason: GAR1 H/ACA snoRNP subunits; conserved. - go_id: GO:0070043 label: rRNA (guanine-N7-)-methyltransferase activity aspect: MF annotations: - UniProtKB:D8SFJ5 (Selaginella, IBA) - UniProtKB:D8TFI1 (Selaginella, IBA) - UniProtKB:F4K7J0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000788684 verdict: FLAG_FAILS reason: RsmG 16S rRNA m7G methyltransferase in plastids; correct bacterial-origin biology. - go_id: GO:0160232 label: INTAC complex aspect: CC annotations: - UniProtKB:D8RL27 (Selaginella, IBA) - UniProtKB:O49433 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000330295 verdict: FLAG_FAILS reason: Integrator INTS7 homologs; Integrator and PP2A are both present in plants, so INTAC is plausible. - go_id: GO:0035539 label: 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity aspect: MF annotations: - UniProtKB:D8RKB0 (Selaginella, IEA) - UniProtKB:Q9CA40 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN001441425; other: ARBA:ARBA00098341, EC:3.6.1.55, RHEA:31575' verdict: FLAG_FAILS reason: Arabidopsis NUDT1 hydrolyses 8-oxo-dGTP; correct. - go_id: GO:0033818 label: beta-ketoacyl-acyl-carrier-protein synthase III activity aspect: MF annotations: - UniProtKB:D8SNT2 (Selaginella, IBA/IEA) - UniProtKB:P49243 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN001823076; other: ARBA:ARBA00086384, EC:2.3.1.180, RHEA:12080' verdict: FLAG_FAILS reason: Plastid FabH (KAS III); correct, plant type II FAS. - go_id: GO:0008760 label: UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity aspect: MF annotations: - UniProtKB:D8RDE2 (Selaginella, IBA/IEA) - UniProtKB:D8RSB4 (Selaginella, IBA/IEA) mechanism: 'IBA PANTHER:PTN000472564; other: EC:2.5.1.7, InterPro:IPR005750' verdict: FLAG_FAILS reason: D8RDE2/D8RSB4 are MurA subfamily enzymes (IPR005750); the activity follows from the conserved enzyme whatever the status of Selaginella plastid peptidoglycan. - go_id: GO:0032267 label: tRNA(Ile)-lysidine synthase activity aspect: MF annotations: - UniProtKB:D8S1U3 (Selaginella, IBA) - UniProtKB:F4J7P7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000211457 verdict: FLAG_FAILS reason: RSY3/TilS lysidine synthase acts on plastid tRNA-Ile; correct. - go_id: GO:0061503 label: tRNA threonylcarbamoyladenosine dehydratase activity aspect: MF annotations: - UniProtKB:D8QP30 (Selaginella, IBA) - UniProtKB:D8SIZ6 (Selaginella, IBA) mechanism: IBA PANTHER:PTN001333297 verdict: FLAG_FAILS reason: TcdA-type dehydratase, same node as GO:0061504. - go_id: GO:0006509 label: membrane protein ectodomain proteolysis aspect: BP annotations: - UniProtKB:D8RGP0 (Selaginella, IBA) - UniProtKB:O64668 (Arabidopsis, IBA) - UniProtKB:Q9SIK7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000024429 verdict: UNCERTAIN reason: Presenilin-like proteins (PTN000024429, seeded by PSEN1/2). Presenilin cuts inside the membrane (GO:0031293 fits gamma-secretase better than ectodomain shedding), and proteolytic activity of plant presenilins is unshown. Settle with a plant gamma-secretase substrate cleavage. - go_id: GO:0097729 label: 9+2 motile cilium aspect: CC annotations: - UniProtKB:D8REA1 (Selaginella, IBA) - UniProtKB:D8STS7 (Selaginella, IBA) - UniProtKB:D8T4D7 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000743491 verdict: FLAG_FAILS reason: Inner-arm dynein heavy chains of Selaginella, whose sperm swim; GO's constraint excludes only seed plants. - go_id: GO:0017177 label: glucosidase II complex aspect: CC annotations: - UniProtKB:Q9FM96 (Arabidopsis, IBA) - UniProtKB:Q9SLC0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000290448 verdict: FLAG_FAILS reason: Glucosidase II beta subunits (PSL4); ER glucosidase II is conserved in plants. - go_id: GO:0033557 label: Slx1-Slx4 complex aspect: CC annotations: - UniProtKB:D8QRY0 (Selaginella, IBA) - UniProtKB:F4IMS6 (Arabidopsis, IEA) mechanism: 'IBA PANTHER:PTN000463591; other: InterPro:IPR027520, UniRule:UR000106239' verdict: UNCERTAIN reason: SLX1 homologs (HIGLE, D8QRY0). No SLX4 family (PTHR21541) member exists in Arabidopsis or Selaginella, so membership of an Slx1-Slx4 complex is unproven; SLX4 is divergent, so settle by identifying the plant SLX1 partner. - go_id: GO:0033565 label: ESCRT-0 complex aspect: CC annotations: - UniProtKB:D8REJ0 (Selaginella, IBA) - UniProtKB:D8RI30 (Selaginella, IBA) mechanism: IBA PANTHER:PTN002493178 verdict: ANNOTATION_WRONG reason: Land plants lack ESCRT-0 (Vps27/Hrs, Hse1/STAM) and use TOL proteins instead. The Selaginella proteins have ankyrin-repeat plus FYVE architecture (Pfam PF12796, PF01363), not the VHS-FYVE-UIM of Vps27, even though PANTHER groups them in PTHR47794. - go_id: GO:0006550 label: L-isoleucine catabolic process aspect: BP annotations: - UniProtKB:D8QMK2 (Selaginella, IBA) - UniProtKB:D8R7M9 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000214535 verdict: FLAG_FAILS reason: Branched-chain aminotransferases; plant mitochondrial BCAA catabolism is real. - go_id: GO:0000388 label: spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) aspect: BP annotations: - UniProtKB:O48534 (Arabidopsis, IBA) - UniProtKB:Q9SYP1 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN002375518 verdict: FLAG_FAILS reason: BRR2 spliceosomal helicase; conserved. - go_id: GO:0034462 label: small-subunit processome assembly aspect: BP annotations: - UniProtKB:D8R652 (Selaginella, IBA) - UniProtKB:D8SGB9 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000267771 verdict: FLAG_FAILS reason: ESF2 SSU processome factor; conserved. - go_id: GO:0008160 label: protein tyrosine phosphatase activator activity aspect: MF annotations: - UniProtKB:D8SYB5 (Selaginella, IBA) - UniProtKB:D8T749 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000000630 verdict: FLAG_FAILS reason: PTPA (PP2A phosphatase activator); the term's tyrosine-phosphatase wording is a family-wide legacy, not a plant-specific error. - go_id: GO:1990529 label: glycosylphosphatidylinositol-mannosyltransferase I complex aspect: CC annotations: - UniProtKB:D8RC64 (Selaginella, IBA) - UniProtKB:Q500W7 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000306537 verdict: FLAG_FAILS reason: PIGM GPI mannosyltransferase I; plants make GPI anchors. - go_id: GO:0071528 label: tRNA re-export from nucleus aspect: BP annotations: - UniProtKB:D8RVE5 (Selaginella, IBA/IEA) - UniProtKB:D8S245 (Selaginella, IBA/IEA) - UniProtKB:Q7PC79 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN000409486; other: InterPro:IPR040017, UniRule:UR001184764' verdict: FLAG_FAILS reason: PAUSED/exportin-t; tRNA nuclear export is conserved. - go_id: GO:0070860 label: RNA polymerase I core factor complex aspect: CC annotations: - UniProtKB:A0A1P8AW93 (Arabidopsis, IEA) - UniProtKB:D8SEQ9 (Selaginella, IEA) - UniProtKB:Q5XVF0 (Arabidopsis, IBA/IEA) mechanism: 'IBA PANTHER:PTN001586581; other: InterPro:IPR033599' verdict: FLAG_FAILS reason: Rrn7/TAF1B is a Pol I core factor subunit; conserved. - go_id: GO:0051306 label: mitotic sister chromatid separation aspect: BP annotations: - UniProtKB:D8QR20 (Selaginella, IBA) - UniProtKB:D8R7W5 (Selaginella, IBA) - UniProtKB:Q9LUR0 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN001285342 verdict: FLAG_FAILS reason: Condensin II CAP-H2; plant condensin II acts in mitotic chromosome resolution. - go_id: GO:0000783 label: nuclear telomere cap complex aspect: CC annotations: - UniProtKB:Q56Y52 (Arabidopsis, IBA) - UniProtKB:Q6NKX5 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000376531 verdict: FLAG_FAILS reason: POT1a/POT1b associate with plant telomeres and CST/telomerase; telomere capping complexes exist in plants. - group: plants_inferred terms: 118 entry_count: 122 verdicts: ANNOTATION_WRONG: 28 CONSTRAINT_QUESTIONABLE: 1 FLAG_FAILS: 54 TRUE_BUT_GENERAL: 17 UNCERTAIN: 22 summary: '118 terms, 122 entries (3 terms split by protein): FLAG_FAILS 54, ANNOTATION_WRONG 28, UNCERTAIN 22, TRUE_BUT_GENERAL 17, CONSTRAINT_QUESTIONABLE 1. Most flags are correct rare plant/lycophyte biology or mechanical GOC MF-to-BP inferences (e.g. PLT5 sugar/polyol transport, 6 terms). The errors cluster in: UniProt SubCell lines carried over from animal homologs (midbody, caveola, phagosome, ERGIC), InterPro2GO entries named for animal/fungal function (Deltex->Notch, HMMR->hyaluronan, Hda2/3->HDA1 complex, podocalyxin, erythromycin esterase->response to antibiotic), over-broad UniRules (RCK_C->K+ channel regulator, PEMT/PLMT->PE methylation), CcmA EC 7.6.2.5 heme export, and legacy TAIR/TIGR TAS/ISS/NAS term choices (calcineurin, integrin, NuRD, epoxygenase pathway, exo- vs endo-glucanase, and an ISS from human caspase-3 to Casparian strip protein CASP3). ARBA rules mostly emit true-but-uninformative grouping terms, and a few emit unsupported ones.' fetched_pmids: - PMID:23944713 - PMID:19366698 entries: - go_id: GO:0043190 label: ATP-binding cassette (ABC) transporter complex aspect: CC annotations: - UniProtKB:D8QQK4 (Selaginella, IEA) - UniProtKB:D8R8C6 (Selaginella, IEA) - UniProtKB:Q8L4R0 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR030802 (MlaE-like permease) verdict: FLAG_FAILS reason: TGD1 is the permease of the chloroplast TGD1/2/3 ABC transporter (MlaE homolog); MlaE permeases sit in MlaFEDB-type ABC complexes, so the mapping holds family-wide. Few plant ABC subunits carry the complex term. - go_id: GO:0015833 label: peptide transport aspect: BP annotations: - UniProtKB:P46032 (Arabidopsis, TAS) mechanism: TAS (TAIR) PMID:9232875 verdict: FLAG_FAILS reason: NPF8.3/PTR2 is a characterized di/tripeptide transporter (UniProt FUNCTION). - go_id: GO:0008658 label: penicillin binding aspect: MF annotations: - UniProtKB:D8R6S4 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR001460 (PBP transpeptidase domain) verdict: FLAG_FAILS reason: D8R6S4 is a bifunctional GT51+transpeptidase PBP; non-seed plants retain plastid peptidoglycan genes, and penicillin binding is a defining property of the transpeptidase domain. - go_id: GO:0005201 label: extracellular matrix structural constituent aspect: MF annotations: - UniProtKB:Q94BT2 (Arabidopsis, TAS) mechanism: TAS (TIGR) PMID:10080694 verdict: ANNOTATION_WRONG reason: AIR12 is a GPI-anchored apoplastic one-heme cytochrome b561-domain protein (UniProt FUNCTION, PubMed:19386804), not a structural constituent of any matrix; a legacy TIGR statement with no structural evidence. - go_id: GO:0008092 label: cytoskeletal protein binding aspect: MF annotations: - UniProtKB:Q9ZSY2 (Arabidopsis, TAS) mechanism: TAS (TAIR) PMID:9927707 verdict: UNCERTAIN reason: ARG1/ATJ15 is a DnaJ protein; the cytoskeletal-binding claim rests on a coiled-coil similarity noted at cloning, not a binding assay. A direct actin/tubulin binding assay would settle it. - go_id: GO:0033553 label: rDNA heterochromatin aspect: CC annotations: - UniProtKB:Q84JC0 (Arabidopsis, ISS) mechanism: ISS (UniProt) from UniProtKB:O43159 human RRP8/nucleomethylin verdict: UNCERTAIN reason: Human NML acts at rDNA chromatin within the mammalian eNoSC (with SIRT1/SUV39H1); the conserved RRP8 activity is rRNA m1A methylation. Whether plant RRP8 has any rDNA-heterochromatin role is untested; a ChIP/localization study would settle it. - go_id: GO:0046677 label: response to antibiotic aspect: BP annotations: - UniProtKB:D8QZA1 (Selaginella, IEA) - UniProtKB:D8RWK2 (Selaginella, IEA) - UniProtKB:D8SMK5 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR007815 (erythromycin esterase) verdict: ANNOTATION_WRONG reason: '''Response to antibiotic'' describes a cell''s response, not an antibiotic-modifying enzyme; the uncharacterized Selaginella homologs have no link to antibiotic exposure. The mapping is a process-for-enzyme misuse across the whole family; propose removal from interpro2go.' - go_id: GO:0030496 label: midbody aspect: CC annotations: - UniProtKB:D8T0K0 (Selaginella, IEA) - UniProtKB:D8TER3 (Selaginella, IEA) mechanism: IEA UniProtKB-SubCell SL-0469 (Midbody), set on the entries by ARBA00004214 verdict: ANNOTATION_WRONG reason: Land plants complete cytokinesis with a phragmoplast and cell plate and form no midbody; the location was carried over by ARBA from animal CEP44. - go_id: GO:0048468 label: cell development aspect: BP annotations: - UniProtKB:F4J8V9 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00028665 (actin) verdict: TRUE_BUT_GENERAL reason: ACT2 is needed for root-hair tip growth, so 'cell development' is true but uninformative; the ARBA rule applies a generic developmental term to actins across kingdoms. replacement: GO:0048767 root hair elongation - go_id: GO:1904047 label: S-adenosyl-L-methionine binding aspect: MF annotations: - UniProtKB:F4KFG1 (Arabidopsis, IEA) - UniProtKB:F4KFG2 (Arabidopsis, IEA) mechanism: IEA UniRule UR000166007 (HAMAP MF_03146 TSR3_euk) verdict: FLAG_FAILS reason: TSR3 transfers the aminocarboxypropyl group from SAM to 18S rRNA, so SAM binding is inherent to the activity. - go_id: GO:0009254 label: peptidoglycan turnover aspect: BP annotations: - UniProtKB:D8RPD8 (Selaginella, IEA) - UniProtKB:D8SM46 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR010611 (3D domain) verdict: UNCERTAIN reason: 'The 3D domain is a small Asp-rich motif from bacterial cell-wall proteins (PANTHER: YocH cell wall-binding family); the same entry also maps ''outer membrane'', which cannot hold for a plant. Peptidoglycan turnover in Selaginella would need plastid PG plus plastid targeting of these proteins; a domain-level process mapping is weak family-wide.' - go_id: GO:0001717 label: conversion of seryl-tRNAsec to selenocys-tRNAsec aspect: BP annotations: - UniProtKB:Q8RWT8 (Arabidopsis, IEA) mechanism: IEA UniProtKB-UniPathway UPA00906 (selenocysteinyl-tRNA(Sec) biosynthesis) verdict: ANNOTATION_WRONG reason: SerRS only makes Ser-tRNA(Sec); the Ser-to-Sec conversion is done by SelA or PSTK/SepSecS. The pathway-to-GO mapping assigns the conversion step to every SerRS, and land plants lack selenocysteine and tRNA(Sec) altogether. - go_id: GO:0015753 label: D-xylose transmembrane transport aspect: BP annotations: - UniProtKB:Q8VZ80 (Arabidopsis, IEA) mechanism: IEA GOC inference (GO_REF:0000108) from GO:0015148 D-xylose TM transporter activity verdict: FLAG_FAILS reason: PLT5 is a broad-spectrum polyol/sugar-proton symporter that transports pentoses including xylose (UniProt FUNCTION); the MF-to-BP inference is mechanical. - go_id: GO:0120025 label: plasma membrane bounded cell projection aspect: CC annotations: - UniProtKB:D8RA45 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00028036 verdict: TRUE_BUT_GENERAL reason: IFT46 is an intraflagellar transport subunit and Selaginella makes flagellated sperm, so a cell-projection location is right but cilium is the informative term. replacement: GO:0005929 cilium - go_id: GO:0043168 label: anion binding aspect: MF annotations: - UniProtKB:F4JXM5 (Arabidopsis, IEA) - UniProtKB:Q9FHN8 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00026944 (generic binding-parent rule) verdict: TRUE_BUT_GENERAL reason: KIN14E/ZWICHEL is a kinesin; 'anion binding' is an uninformative parent of ATP binding produced by an ARBA rule (same rule family as GO:1901363). replacement: GO:0005524 ATP binding - go_id: GO:0055086 label: nucleobase-containing small molecule metabolic process aspect: BP annotations: - UniProtKB:Q9S847 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00027681 verdict: TRUE_BUT_GENERAL reason: 'CDA3 is a cytidine deaminase (UniProt FUNCTION: scavenges cytidine for UMP synthesis); the grouping term is true but uninformative.' replacement: GO:0008655 pyrimidine-containing compound salvage - go_id: GO:0006220 label: pyrimidine nucleotide metabolic process aspect: BP annotations: - UniProtKB:D8RFM2 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR016473 (dCMP deaminase) verdict: FLAG_FAILS reason: dCMP deaminase is a pyrimidine nucleotide metabolic enzyme; mapping sound family-wide. - go_id: GO:0008305 label: integrin complex aspect: CC annotations: - UniProtKB:P0DI79 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:10196471, no with/from verdict: ANNOTATION_WRONG reason: At14a (UPF0496 family) was named for partial similarity to integrin beta; plants have no integrin alpha/beta heterodimers, so membership of an integrin complex cannot apply. - go_id: GO:0033116 label: endoplasmic reticulum-Golgi intermediate compartment membrane aspect: CC annotations: - UniProtKB:Q9SIN7 (Arabidopsis, IEA) mechanism: IEA UniProtKB-SubCell SL-0099, from HAMAP MF_03058 (VMA21) verdict: ANNOTATION_WRONG reason: The HAMAP VMA21 rule adds an ERGIC location from animal VMA21; plant ER export sites couple directly to Golgi stacks without an established ERGIC. Keep the ER membrane location from the same rule; restrict the ERGIC line of MF_03058 to Metazoa. replacement: GO:0005789 endoplasmic reticulum membrane - go_id: GO:1902495 label: transmembrane transporter complex aspect: CC annotations: - UniProtKB:Q94JS0 (Arabidopsis, IEA) - UniProtKB:Q9LYR2 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00026587 verdict: TRUE_BUT_GENERAL reason: UCR1-1/UCR1-2 are Rieske subunits of complex III, which is a transmembrane transporter complex in GO (respiratory chain complex III is_a descendant), but the specific complex term fits. replacement: GO:0045275 respiratory chain complex III - go_id: GO:1902495 label: transmembrane transporter complex aspect: CC annotations: - UniProtKB:Q9ZUT3 (Arabidopsis, IEA) mechanism: IEA Ensembl Compara projection (GO_REF:0000107) from rice STAR2 UniProtKB:Q5W7C1 verdict: TRUE_BUT_GENERAL reason: ALS3 is the STAR2-type permease partner of a bacterial-type ABC transporter; the complex term is right and the ABC transporter complex term is more specific. replacement: GO:0043190 ATP-binding cassette (ABC) transporter complex - go_id: GO:0140331 label: aminophospholipid translocation aspect: BP annotations: - UniProtKB:Q9XIE6 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015247 aminophospholipid flippase activity verdict: FLAG_FAILS reason: ALA3 is a P4-ATPase lipid flippase (UniProt FUNCTION); mechanical MF-to-BP inference. - go_id: GO:0004865 label: protein serine/threonine phosphatase inhibitor activity aspect: MF annotations: - UniProtKB:Q8S8F7 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR011107 (type 1 PP inhibitor) verdict: FLAG_FAILS reason: INH3 binds and inhibits PP1 (UniProt FUNCTION, PubMed:19329567); mapping sound. - go_id: GO:0007219 label: Notch signaling pathway aspect: BP annotations: - UniProtKB:D8QPY5 (Selaginella, IEA) - UniProtKB:D8SKI6 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR039398 (Deltex family) verdict: ANNOTATION_WRONG reason: Plants have no Notch receptor or ligands; the Deltex-family mapping holds only for metazoan members. Recommend a Metazoa-only taxon constraint on GO:0007219 (currently only never_in Fungi) or restricting the interpro2go row. - go_id: GO:0051049 label: regulation of transport aspect: BP annotations: - UniProtKB:D8R2Q2 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00027251 verdict: UNCERTAIN reason: D8R2Q2 is an uncharacterized AGC kinase (PANTHER S6 kinase family); the ARBA rule pools many unrelated animal conditions onto a vague regulatory process with no evidence for this protein. The term could be true of the protein; the defect is that the ARBA rule asserts it without basis, so the row is unsupported rather than shown wrong. - go_id: GO:0015459 label: potassium channel regulator activity aspect: MF annotations: - UniProtKB:D8RMS5 (Selaginella, IEA) mechanism: IEA UniRule UR000414538 (PROSITE PS51202 RCK C-terminal domain, all taxa) verdict: ANNOTATION_WRONG reason: D8RMS5 is a DASS/YfcC-type antiporter (IPR004680, PANTHER basic amino acid antiporter YfcC-related) that carries RCK_C domains, not a channel subunit. The rule maps any RCK_C domain to K+ channel regulation, which is wrong for every transporter family that carries the domain; restrict it to channel/Ktr/Trk contexts. - go_id: GO:0098552 label: side of membrane aspect: CC annotations: - UniProtKB:D8QNF6 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00027303 verdict: TRUE_BUT_GENERAL reason: D8QNF6 is a stomatin-like protein 2 homolog (PANTHER SLP2 mitochondrial); 'side of membrane' is an uninformative ARBA output, and its mitochondrial inner-membrane location is the informative one (by homology). replacement: GO:0005743 mitochondrial inner membrane - go_id: GO:0035235 label: ionotropic glutamate receptor signaling pathway aspect: BP annotations: - UniProtKB:Q9C8E7 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0022849 glutamate-gated calcium ion channel activity verdict: CONSTRAINT_QUESTIONABLE reason: GLR3.3 is a glutamate-gated cation channel whose opening by glutamate drives Ca2+ signalling, matching the term definition (ligand binding, ion flux through the receptor, downstream regulation). The only_in Metazoa constraint looks too narrow for plant GLRs; the GOC inference rule bypassed it. - go_id: GO:0008333 label: endosome to lysosome transport aspect: BP annotations: - UniProtKB:Q9FG38 (Arabidopsis, TAS) mechanism: TAS (TAIR) PMID:17999644 verdict: ANNOTATION_WRONG reason: SNX1 mediates endosome-to-vacuole sorting (UniProt FUNCTION); plants have lytic vacuoles, not lysosomes, so the term choice is wrong for the lineage. replacement: GO:0045324 late endosome to vacuole transport - go_id: GO:0042242 label: cobyrinic acid a,c-diamide synthase activity aspect: MF annotations: - UniProtKB:D8S6S2 (Selaginella, IEA) - UniProtKB:D8SNL9 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR004484 (CbiA/CobB) verdict: ANNOTATION_WRONG reason: Plants do not synthesize cobalamin and Selaginella has no other cobalamin-biosynthesis proteins in UniProt (KW-0169 query empty), so the substrate does not exist; either these are diverged paralogs or assembly contaminants. The mapping is fine for true CbiA/CobB. - go_id: GO:0004715 label: non-membrane spanning protein tyrosine kinase activity aspect: MF annotations: - UniProtKB:Q8L4H0 (Arabidopsis, IEA) mechanism: IEA EC:2.7.10.2 mapping (GO_REF:0000003) verdict: FLAG_FAILS reason: Plant WEE1 is a nuclear Tyr15 CDK kinase; the EC-to-GO mapping is right. - go_id: GO:0004715 label: non-membrane spanning protein tyrosine kinase activity aspect: MF annotations: - UniProtKB:Q9LSC2 (Arabidopsis, IEA) mechanism: IEA EC:2.7.10.2; EC itself from PROSITE ProRule PRU10028 (Tyr kinase active-site pattern) verdict: UNCERTAIN reason: At3g15890 is a PTI1-like plant TKL kinase whose EC 2.7.10.2 comes only from the PS00109 pattern, which also matches Ser/Thr TKL kinases; no tyrosine phosphorylation is reported. A kinase assay with Tyr substrates would settle it. - go_id: GO:0004715 label: non-membrane spanning protein tyrosine kinase activity aspect: MF annotations: - UniProtKB:F4HVG8 (Arabidopsis, IEA) mechanism: IEA EC:2.7.10.2 mapping verdict: UNCERTAIN reason: CSK is a modified two-component sensor kinase whose autophosphorylation was assigned 'probably on a tyrosine residue' (UniProt FUNCTION, PubMed:18632566); the EC rests on that tentative call. Mapping the phosphoamino acid would settle it. - go_id: GO:0002682 label: regulation of immune system process aspect: BP annotations: - UniProtKB:A0A1P8AXJ0 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00027003 verdict: UNCERTAIN reason: A Rab7 GTPase (RABG3) gets an immune-regulation term from a multi-condition ARBA rule learned from animal annotations; no immune role is reported for this protein. The term could be true of the protein; the defect is that the ARBA rule asserts it without basis, so the row is unsupported rather than shown wrong. - go_id: GO:0030867 label: rough endoplasmic reticulum membrane aspect: CC annotations: - UniProtKB:Q94BX4 (Arabidopsis, ISS) mechanism: ISS (UniProt) from UniProtKB:P37287 human PIGA verdict: FLAG_FAILS reason: PIGA is the catalytic subunit of the ER GPI-GlcNAc transferase; plants have rough ER and the transfer is reasonable. - go_id: GO:0009264 label: deoxyribonucleotide catabolic process aspect: BP annotations: - UniProtKB:F4JVY6 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR010708 (5'(3')-deoxyribonucleotidase) verdict: FLAG_FAILS reason: At4g33140 is a member of the NT5C-like deoxyribonucleotidase family (also PANTHER YqfW-related nucleotidase); the family mapping is sound though the plant enzyme is untested. - go_id: GO:0019854 label: L-ascorbic acid catabolic process aspect: BP annotations: - UniProtKB:Q8LPL3 (Arabidopsis, IEA) mechanism: IEA UniProtKB-UniPathway UPA00263 (L-ascorbate degradation) verdict: FLAG_FAILS reason: Ascorbate oxidase oxidizes apoplastic ascorbate, the entry step of its oxidative breakdown; plausible for a plant-abundant enzyme. - go_id: GO:0015752 label: D-ribose transmembrane transport aspect: BP annotations: - UniProtKB:Q8VZ80 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015591 D-ribose TM transporter activity verdict: FLAG_FAILS reason: PLT5 transports pentoses including ribose (UniProt FUNCTION); mechanical inference. - go_id: GO:0033993 label: response to lipid aspect: BP annotations: - UniProtKB:D8SX49 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00028073 verdict: UNCERTAIN reason: An uncharacterized Selaginella CPA2/KEA-type cation:proton antiporter gets 'response to lipid' from a pooled ARBA rule; no basis for this protein. The term could be true of the protein; the defect is that the ARBA rule asserts it without basis, so the row is unsupported rather than shown wrong. - go_id: GO:1902603 label: carnitine transmembrane transport aspect: BP annotations: - UniProtKB:Q9CAT6 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015226 carnitine transmembrane transporter activity verdict: FLAG_FAILS reason: OCT1 is a high-affinity carnitine transporter (UniProt FUNCTION, PubMed:17521409). - go_id: GO:0008710 label: 8-amino-7-oxononanoate synthase activity aspect: MF annotations: - UniProtKB:Q8GW43 (Arabidopsis, IEA) mechanism: IEA EC:2.3.1.47 mapping verdict: FLAG_FAILS reason: BIOF is the experimentally characterized plant AONS (UniProt FUNCTION, PubMed:16299174); biotin synthesis is real in plants. - go_id: GO:0141093 label: 5-amino-6-(D-ribitylamino)uracil--L-tyrosine 4-hydroxyphenyl transferase activity aspect: MF annotations: - UniProtKB:D8RBF3 (Selaginella, IEA) mechanism: IEA EC:2.5.1.147 mapping verdict: FLAG_FAILS reason: D8RBF3 is a fused CofG/CofH FO synthase (796 aa); FO is used as a photolyase antenna chromophore in green lineages, so the activity is plausible rare biology. - go_id: GO:0140588 label: chromatin looping aspect: BP annotations: - UniProtKB:A5HEI1 (Arabidopsis, IEA) - UniProtKB:D8RFB7 (Selaginella, IEA) - UniProtKB:D8SDH0 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR033031 (Scc2/Nipped-B) verdict: FLAG_FAILS reason: SCC2 is the cohesin loader, required for cohesin-mediated loop extrusion; mapping sound family-wide. - go_id: GO:0035351 label: heme transmembrane transport aspect: BP annotations: - UniProtKB:Q9C8T1 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015439 ABC-type heme transporter activity (itself from EC:7.6.2.5/RHEA:19261) verdict: ANNOTATION_WRONG reason: Inherits the heme-export MF of CcmA (see GO:0015439); UniProt itself states CcmAB does not seem to export heme. - go_id: GO:1901264 label: carbohydrate derivative transport aspect: BP annotations: - UniProtKB:D8RD67 (Selaginella, IEA) - UniProtKB:D8RFA2 (Selaginella, IEA) mechanism: IEA GOC inference from GO:0005338 nucleotide-sugar TM transporter activity verdict: TRUE_BUT_GENERAL reason: Correct parent of the transporters' nucleotide-sugar transport; the specific term fits. replacement: GO:0015780 nucleotide-sugar transmembrane transport - go_id: GO:0036104 label: Kdo2-lipid A biosynthetic process aspect: BP annotations: - UniProtKB:Q8VZA5 (Arabidopsis, IEA) mechanism: IEA UniProtKB-UniPathway UPA00360 verdict: FLAG_FAILS reason: Arabidopsis synthesizes lipid A precursors via the E. coli pathway (RAR project); the repo KDTA review ACCEPTs this row. - go_id: GO:1990426 label: mitotic recombination-dependent replication fork processing aspect: BP annotations: - UniProtKB:A0A1P8BGT9 (Arabidopsis, IEA) - UniProtKB:P94102 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR011941 (Rad51) verdict: FLAG_FAILS reason: RAD51-mediated recombination at stalled forks is conserved; the term is rare in plants only because it was coined from fission-yeast curation. - go_id: GO:0005901 label: caveola aspect: CC annotations: - UniProtKB:Q4V3D6 (Arabidopsis, IEA) - UniProtKB:Q501E6 (Arabidopsis, IEA) - UniProtKB:Q9LV90 (Arabidopsis, IEA) mechanism: IEA UniProtKB-SubCell SL-0035 (Caveola) verdict: ANNOTATION_WRONG reason: Plants have no caveolins and no caveolae; plant flotillins are in plasma-membrane nanodomains/detergent-resistant membranes (UniProt, PubMed:15618420). The current UniProt entries now say only 'Cell membrane', so the GOA row is stale. replacement: GO:0045121 membrane raft - go_id: GO:0051239 label: regulation of multicellular organismal process aspect: BP annotations: - UniProtKB:Q9M8Z5 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00028859 verdict: TRUE_BUT_GENERAL reason: NSN1 is a nucleolar YlqF-type GTPase whose loss alters meristem and flower development (UniProt FUNCTION); the ARBA term is true but a pleiotropic, very general phenotype. replacement: GO:0009909 regulation of flower development - go_id: GO:0051239 label: regulation of multicellular organismal process aspect: BP annotations: - UniProtKB:D8RNZ2 (Selaginella, IEA) - UniProtKB:D8SXB6 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00028859 verdict: UNCERTAIN reason: The Selaginella CP-type GTPases inherit a developmental-phenotype term from an ARBA rule; nothing is known of their roles. - go_id: GO:0004303 label: estradiol 17-beta-dehydrogenase [NAD(P)+] activity aspect: MF annotations: - UniProtKB:P0DKC5 (Arabidopsis, IEA) mechanism: IEA RHEA:24616 mapping verdict: FLAG_FAILS reason: 17beta-estradiol oxidation by HSD1 was measured (UniProt CATALYTIC ACTIVITY, ECO:0000269 PubMed:17074428); the mapping is faithful, though the physiological substrate in plants is likely another steroid. - go_id: GO:0042355 label: L-fucose catabolic process aspect: BP annotations: - UniProtKB:Q9LJK1 (Arabidopsis, NAS) mechanism: NAS (UniProt) PMID:11698403 verdict: ANNOTATION_WRONG reason: FUT11 adds core alpha1,3-fucose to N-glycans (UniProt FUNCTION), which is glycan synthesis, not fucose breakdown; the cited paper is a Drosophila proteome survey. replacement: GO:0006487 protein N-linked glycosylation supported_by: - reference_id: PMID:11698403 supporting_text: Composition of Drosophila melanogaster proteome involved in fucosylated glycan - go_id: GO:0008677 label: 2-dehydropantoate 2-reductase activity aspect: MF annotations: - UniProtKB:F4KIN4 (Arabidopsis, IEA/TAS) mechanism: IEA EC:1.1.1.169 / RHEA:16233; TAS (TAIR) PMID:14675432 verdict: FLAG_FAILS reason: Plants synthesize pantothenate and KPR is the ketopantoate reductase candidate in that pathway; mappings are faithful. - go_id: GO:0047809 label: D-lactate dehydrogenase activity aspect: MF annotations: - UniProtKB:Q94AX4 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00093753 verdict: TRUE_BUT_GENERAL reason: AtD-LDH oxidizes D-lactate with cytochrome c as acceptor (UniProt name and FUNCTION); the generic acceptor term is a parent. replacement: GO:0004458 D-lactate dehydrogenase (cytochrome) activity - go_id: GO:0004114 label: 3',5'-cyclic-nucleotide phosphodiesterase activity aspect: MF annotations: - UniProtKB:D8T0K1 (Selaginella, IEA) - UniProtKB:D8TER4 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR002073 + IPR036971 (PDE catalytic domain) verdict: FLAG_FAILS reason: D8T0K1/D8TER4 fuse a class-III nucleotidyl cyclase with a PDE domain, an architecture kept in plants with motile sperm; both domain mappings are standard. - go_id: GO:0009190 label: cyclic nucleotide biosynthetic process aspect: BP annotations: - UniProtKB:D8T0K1 (Selaginella, IEA) - UniProtKB:D8TER4 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR001054 (class-3/4 AC/GC domain) verdict: FLAG_FAILS reason: Same cyclase-PDE fusion proteins as GO:0004114; the cyclase domain mapping is standard. - go_id: GO:0045335 label: phagocytic vesicle aspect: CC annotations: - UniProtKB:Q8VY27 (Arabidopsis, IEA) - UniProtKB:Q9FGH9 (Arabidopsis, IEA) - UniProtKB:Q9LMJ4 (Arabidopsis, IEA) mechanism: IEA UniProtKB-SubCell SL-0206 (Phagosome); EXO70B1 curated from PubMed:23944713, B2/H1 by similarity to EXO70B1 verdict: ANNOTATION_WRONG reason: Plant cells do not phagocytose. The cited study shows EXO70B1 compartments colocalize with the autophagosome marker ATG8f, so UniProt's 'phagosome' should be 'autophagosome' (source error propagated to B2 and H1). replacement: GO:0005776 autophagosome supported_by: - reference_id: PMID:23944713 supporting_text: EXO70B1 positive compartments are internalized into the central vacuole and co-localize with autophagosomal marker ATG8f. - go_id: GO:0102521 label: tRNA-4-demethylwyosine synthase activity aspect: MF annotations: - UniProtKB:D8RBB7 (Selaginella, IEA) - UniProtKB:Q8RXN5 (Arabidopsis, IEA) mechanism: IEA EC:4.1.3.44 / RHEA:36347 verdict: FLAG_FAILS reason: TYW1 makes the wyosine core of tRNA-Phe, a eukaryote-wide modification; mapping sound. - go_id: GO:0030301 label: cholesterol transport aspect: BP annotations: - UniProtKB:F4I9G5 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00034167 (NPC1) verdict: UNCERTAIN reason: Plant NPC1 homologs are linked to sphingolipid homeostasis, and cholesterol is a minor plant sterol; sterol binding or transport by AtNPC1 has not been shown here. A sterol-binding assay on the NPC1 N-terminal domain would settle it. - go_id: GO:0035873 label: lactate transmembrane transport aspect: BP annotations: - UniProtKB:Q8W037 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015129 lactate TM transporter activity verdict: FLAG_FAILS reason: NIP2;1 is the anoxia-induced lactic acid channel; mechanical inference. - go_id: GO:0043101 label: purine-containing compound salvage aspect: BP annotations: - UniProtKB:D8T0J1 (Selaginella, IEA) mechanism: IEA ARBA:ARBA00084372 verdict: TRUE_BUT_GENERAL reason: HPRT salvages hypoxanthine/guanine to IMP/GMP; the grouping term is right but uninformative. replacement: GO:0032263 GMP salvage - go_id: GO:0008959 label: phosphate acetyltransferase activity aspect: MF annotations: - UniProtKB:D8RE38 (Selaginella, IEA) mechanism: IEA EC:2.3.1.8 mapping verdict: FLAG_FAILS reason: Selaginella encodes both Pta and acetate kinase (D8REZ0, D8SD58), the algal-type Pta-Ack pathway; rare in land plants but real. - go_id: GO:0005955 label: calcineurin complex aspect: CC annotations: - UniProtKB:O81223 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:9632394, from yeast calcineurin B similarity verdict: ANNOTATION_WRONG reason: Plants have no calcineurin catalytic subunit; SOS3/CBL4 activates CIPK kinase SOS2. The repo CBL4 review already REMOVEs this row. - go_id: GO:0015825 label: L-serine transport aspect: BP annotations: - UniProtKB:Q42400 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015194 L-serine TM transporter activity verdict: FLAG_FAILS reason: AAP1 is a broad neutral amino acid-proton symporter; mechanical inference. - go_id: GO:0022407 label: regulation of cell-cell adhesion aspect: BP annotations: - UniProtKB:D8RBM1 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR017403 (Podocalyxin) verdict: ANNOTATION_WRONG reason: Podocalyxin is a vertebrate CD34-family sialomucin; a 1450-aa uncharacterized Selaginella protein matching its family signature (the only PANTHER PTHR12067 hit in Viridiplantae besides one fragment) carries no adhesion evidence, and plant cells are joined by walls, not adhesion molecules of this kind. - go_id: GO:1902555 label: endoribonuclease complex aspect: CC annotations: - UniProtKB:D8QZY1 (Selaginella, IEA) - UniProtKB:D8TC13 (Selaginella, IEA) - UniProtKB:Q6AWV1 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00033555 verdict: TRUE_BUT_GENERAL reason: POP5 is a shared subunit of RNase P and RNase MRP, which are endoribonuclease complexes; the specific complexes fit. replacement: GO:0005655 nucleolar ribonuclease P complex; GO:0000172 ribonuclease MRP complex - go_id: GO:0009349 label: riboflavin synthase complex aspect: CC annotations: - UniProtKB:D8SBQ1 (Selaginella, IEA) - UniProtKB:D8T5Z8 (Selaginella, IEA) - UniProtKB:O80575 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR002180 + IPR036467; UniRule UR000000683 (Pfam PF00885, Eukaryota) verdict: UNCERTAIN reason: These are lumazine synthases. The term fits the Bacillus heavy riboflavin synthase, where a lumazine synthase capsid encloses riboflavin synthase; whether plant lumazine synthase capsids enclose riboflavin synthase is not established. A co-purification of plant RibH with RibE would settle it; riboflavin biosynthetic process is safe. - go_id: GO:0005540 label: hyaluronic acid binding aspect: MF annotations: - UniProtKB:D8RL02 (Selaginella, IEA) - UniProtKB:D8T2S2 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR026203 (IHABP = HMMR/RHAMM family) verdict: ANNOTATION_WRONG reason: Plants make no hyaluronan; the Selaginella HMMR-family homologs (no Arabidopsis members) cannot bind a polymer absent from the lineage. Mapping valid at most for vertebrate HMMR. - go_id: GO:0015795 label: sorbitol transmembrane transport aspect: BP annotations: - UniProtKB:Q8VZ80 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015576 sorbitol TM transporter activity verdict: FLAG_FAILS reason: PLT5 transports sorbitol (UniProt FUNCTION); mechanical inference. - go_id: GO:0019146 label: arabinose-5-phosphate isomerase activity aspect: MF annotations: - UniProtKB:Q9M1T1 (Arabidopsis, IEA) mechanism: IEA EC:5.3.1.13 / RHEA:23104 verdict: FLAG_FAILS reason: Plants make Kdo for rhamnogalacturonan II, which needs A5P isomerase; SETH3 is the GutQ/KpsF-family candidate. - go_id: GO:0001664 label: G protein-coupled receptor binding aspect: MF annotations: - UniProtKB:D8QR00 (Selaginella, IEA) - UniProtKB:D8R7Y3 (Selaginella, IEA) - UniProtKB:P18064 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR002976 (plant G alpha); UniRule UR001591782 (PRINTS PR01242, Viridiplantae only) verdict: UNCERTAIN reason: Both sources are plant-specific and assert GPCR binding for plant Galpha, yet AtGPA1 exchanges nucleotide spontaneously and is regulated by the 7TM-RGS protein RGS1; canonical GEF-type GPCRs are not established in plants (GCR1 binding is reported but disputed as a GPCR). A demonstration of receptor-catalysed exchange would settle it; if none, both plant-only rules should drop the term. - go_id: GO:0016581 label: NuRD complex aspect: CC annotations: - UniProtKB:Q4PSK1 (Arabidopsis, ISS) - UniProtKB:Q8LA53 (Arabidopsis, ISS) mechanism: ISS (UniProt) from human MBD3 UniProtKB:O95983 and MBD2 UniProtKB:Q9UBB5 verdict: ANNOTATION_WRONG reason: AtMBD2/AtMBD3 share only the MBD domain with human MBD2/3 and were named by domain; plants lack the MTA and GATAD2 core subunits that define NuRD, so complex membership was transferred across non-orthologs. - go_id: GO:0098703 label: calcium ion import across plasma membrane aspect: BP annotations: - UniProtKB:D8RLL1 (Selaginella, IEA) - UniProtKB:D8RN34 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR024338 (MID1/Yam8) verdict: UNCERTAIN reason: D8RLL1/D8RN34 match the fungal Mid1 family (Pfam PF12929, PANTHER MID1P) but are 176-237 aa against ~550 aa for yeast Mid1; whether they form a Ca2+ influx channel is unknown. Gene-model checking and a Ca2+ uptake assay would settle it. - go_id: GO:0110078 label: TTT Hsp90 cochaperone complex aspect: CC annotations: - UniProtKB:D8RP92 (Selaginella, IEA) - UniProtKB:D8SM01 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR018870 (Tti2) verdict: FLAG_FAILS reason: TTT (Tel2-Tti1-Tti2) is conserved in eukaryotes including plants; mapping sound. - go_id: GO:0090266 label: regulation of mitotic cell cycle spindle assembly checkpoint aspect: BP annotations: - UniProtKB:F4K991 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR026182 (APC15) verdict: UNCERTAIN reason: At5g63135 (99 aa) matches the APC15 Pfam; APC15's checkpoint-silencing role is shown in fungi and animals, not plants. Showing it co-purifies with the plant APC would settle it. - go_id: GO:0047496 label: vesicle transport along microtubule aspect: BP annotations: - UniProtKB:Q8VWI7 (Arabidopsis, TAS) mechanism: TAS (UniProt) PMID:11701879 verdict: FLAG_FAILS reason: KIN10A/PAKRP2 is a phragmoplast kinesin implicated in Golgi-vesicle transport (UniProt FUNCTION, ECO:0000269 PubMed:11701879). - go_id: GO:1990822 label: basic amino acid transmembrane transport aspect: BP annotations: - UniProtKB:Q39134 (Arabidopsis, IEA) - UniProtKB:Q8GUM3 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015174 basic amino acid TM transporter activity verdict: FLAG_FAILS reason: AAP3 and AAP5 transport basic amino acids (UniProt FUNCTION); mechanical inference. - go_id: GO:0006649 label: phospholipid transfer to membrane aspect: BP annotations: - UniProtKB:Q9S7I3 (Arabidopsis, NAS) mechanism: NAS (TAIR) PMID:10940464 verdict: ANNOTATION_WRONG reason: LTP2 is a secreted apoplastic nsLTP linked to cuticle deposition; the term means intracellular delivery of phospholipid from its site of synthesis to the plasma membrane, which an extracellular protein cannot do. In vitro intermembrane transfer is not this process. - go_id: GO:0015886 label: heme transport aspect: BP annotations: - UniProtKB:F4IL76 (Arabidopsis, IEA) - UniProtKB:F4IL90 (Arabidopsis, IEA) - UniProtKB:F4IMA2 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR003557 (CcmC), IPR003567/IPR003569 (CcmF-type) verdict: UNCERTAIN reason: These are At2g07xxx CcmC/CcmF-family copies (F4IL76 carries a UniRule caution for missing conserved residues). Whether System I CcmC or CcmF moves heme across the membrane is unresolved, unlike System II CcsBA; the mapping is reasonable only for heme exporters. Biochemical evidence for CcmC heme translocation would settle it family-wide. - go_id: GO:0004723 label: calcium-dependent protein serine/threonine phosphatase activity aspect: MF annotations: - UniProtKB:O81223 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:9632394 verdict: ANNOTATION_WRONG reason: CBL4/SOS3 is a calcium-sensor regulatory protein with no phosphatase domain; it activates the CIPK kinase SOS2. The repo CBL4 review REMOVEs this row. supported_by: - reference_id: PMID:9632394 supporting_text: SOS3 encodes a protein that shares significant sequence similarity with the calcineurin B subunit from yeast and neuronal calcium sensors from animals. - go_id: GO:0016422 label: mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity aspect: MF annotations: - UniProtKB:O65090 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:9596631 verdict: ANNOTATION_WRONG reason: PFC1 is a KsgA/Dim1-type rRNA dimethyltransferase methylating plastid 16S rRNA 3' adenosines (UniProt FUNCTION, PubMed:9596631), not the mRNA cap m6Am methyltransferase (PCIF1 activity). replacement: GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity - go_id: GO:0070899 label: mitochondrial tRNA wobble uridine modification aspect: BP annotations: - UniProtKB:Q9SHS2 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00086587 (FunFam, Eukaryota) verdict: UNCERTAIN reason: At2g13440 is the single Arabidopsis MnmG/GidA homolog; wobble cmnm5U modification is right, but whether it acts in mitochondria, plastids or both is unknown. Localization would settle it. - go_id: GO:0004608 label: phosphatidylethanolamine N-methyltransferase activity aspect: MF annotations: - UniProtKB:Q9SAH5 (Arabidopsis, IEA) mechanism: IEA UniRule UR000345849 (HAMAP MF_03216, PEMT/PLMT, Eukaryota) verdict: ANNOTATION_WRONG reason: Arabidopsis PLMT methylates PMME and PDME but cannot use PE (Keogh 2009). MF_03216 pools mammalian PEMT (all three methylations) with plant PLMT; the PE step should be limited to the PEMT/opisthokont branch. replacement: GO:0000773 phosphatidyl-N-methylethanolamine N-methyltransferase activity supported_by: - reference_id: PMID:19366698 supporting_text: plant PLMTs methylate phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine but cannot utilize phosphatidylethanolamine as a substrate - go_id: GO:0004338 label: glucan exo-1,3-beta-glucosidase activity aspect: MF annotations: - UniProtKB:O49353 (Arabidopsis, TAS) - UniProtKB:P33157 (Arabidopsis, ISS) mechanism: TAS (TAIR) PMID:10092183 (BG5); ISS (TAIR) PMID:1392589 (BG2) verdict: ANNOTATION_WRONG reason: BG2 and BG5 are GH17 glucan endo-1,3-beta-glucosidases (EC 3.2.1.39, UniProt names); the exo term is the wrong activity. replacement: GO:0042973 glucan endo-1,3-beta-D-glucosidase activity - go_id: GO:0070823 label: HDA1 complex aspect: CC annotations: - UniProtKB:D8T4Y8 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR021006 (Hda2/Hda3, fungal) verdict: ANNOTATION_WRONG reason: D8T4Y8 is a MOM1-family SNF2 helicase (PANTHER MOM1); InterPro describes IPR021006 as the fungal Hda2/Hda3 subunits, and the HDA1 complex is fungal. The match is a shared domain; restrict the mapping to Fungi. - go_id: GO:0042350 label: GDP-L-fucose biosynthetic process aspect: BP annotations: - UniProtKB:F4I938 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0050577 GDP-L-fucose synthase activity verdict: FLAG_FAILS reason: GER2 is a GDP-L-fucose synthase; mechanical inference. - go_id: GO:0070626 label: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity aspect: MF annotations: - UniProtKB:D8QZE4 (Selaginella, IEA) - UniProtKB:D8RWG5 (Selaginella, IEA) - UniProtKB:F4I1L9 (Arabidopsis, IEA) mechanism: IEA RHEA:23920 mapping verdict: FLAG_FAILS reason: Adenylosuccinate lyase catalyses both the SAICAR and adenylosuccinate cleavages in all purine-synthesizing organisms. - go_id: GO:0004070 label: aspartate carbamoyltransferase activity aspect: MF annotations: - UniProtKB:D8SVC7 (Selaginella, IEA) - UniProtKB:D8T0T6 (Selaginella, IEA) - UniProtKB:P49077 (Arabidopsis, IEA/ISS) mechanism: IEA InterPro2GO IPR002082; EC:2.1.3.2; RHEA:20013; ISS from E. coli PyrB verdict: FLAG_FAILS reason: PYRB is the plant ATCase of de novo pyrimidine synthesis; the low plant rate is a counting artefact. - go_id: GO:0003998 label: acylphosphatase activity aspect: MF annotations: - UniProtKB:D8RM90 (Selaginella, IEA) - UniProtKB:D8S2J6 (Selaginella, IEA) - UniProtKB:Q9LZF2 (Arabidopsis, IEA) mechanism: IEA InterPro2GO IPR020456; EC:3.6.1.7; RHEA:14965 verdict: FLAG_FAILS reason: Acylphosphatase-family proteins; the family mapping is sound. - go_id: GO:0004048 label: anthranilate phosphoribosyltransferase activity aspect: MF annotations: - UniProtKB:D8R2J8 (Selaginella, IEA) - UniProtKB:D8ST47 (Selaginella, IEA) - UniProtKB:Q02166 (Arabidopsis, IEA/TAS) mechanism: IEA InterPro2GO IPR005940; EC:2.4.2.18; RHEA:11768; TAS PMID:9017401 verdict: FLAG_FAILS reason: PAT1 is the plant tryptophan-pathway anthranilate PRTase. - go_id: GO:0015232 label: heme transmembrane transporter activity aspect: MF annotations: - UniProtKB:F4IL76 (Arabidopsis, IEA) - UniProtKB:F4IL90 (Arabidopsis, IEA) - UniProtKB:F4IMA2 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR003557 (CcmC), IPR003567/IPR003569 (CcmF-type) verdict: UNCERTAIN reason: Same mapping and proteins as GO:0015886; a heme transmembrane transporter activity for System I CcmC/CcmF is not established. - go_id: GO:0120293 label: dynein axonemal particle aspect: CC annotations: - UniProtKB:D8RR31 (Selaginella, IEA) mechanism: IEA UniProtKB-SubCell SL-0542, set by ARBA00024190 verdict: FLAG_FAILS reason: Selaginella builds motile sperm flagella, and axonemal dynein intermediate chains pre-assemble in cytoplasmic DynAPs; plausible rare biology. - go_id: GO:1901363 label: heterocyclic compound binding aspect: MF annotations: - UniProtKB:F4JXM5 (Arabidopsis, IEA) - UniProtKB:Q9FHN8 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00027813 (generic binding-parent rule) verdict: TRUE_BUT_GENERAL reason: Same kinesin and same rule family as GO:0043168; uninformative parent of ATP binding. replacement: GO:0005524 ATP binding - go_id: GO:0046655 label: folic acid metabolic process aspect: BP annotations: - UniProtKB:Q9SPK5 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00091997 verdict: ANNOTATION_WRONG reason: Formate-THF ligase acts on tetrahydrofolate in one-carbon metabolism, not on folic acid (oxidized pteroylglutamate) as the term defines; wrong sibling term. replacement: GO:0035999 folate cycle - go_id: GO:0015439 label: ABC-type heme transporter activity aspect: MF annotations: - UniProtKB:Q9C8T1 (Arabidopsis, IEA) mechanism: IEA EC:7.6.2.5 and RHEA:19261 mapping verdict: ANNOTATION_WRONG reason: UniProt's own FUNCTION says CcmA/ABCI1 was once thought to export heme but does not seem to; the EC 7.6.2.5 assignment is a legacy name carried by the whole CcmA family. Flag EC 7.6.2.5 on CcmA entries upstream. - go_id: GO:0004123 label: cystathionine gamma-lyase activity aspect: MF annotations: - UniProtKB:F4K5T2 (Arabidopsis, IEA) mechanism: IEA RHEA:14005 mapping verdict: FLAG_FAILS reason: DES1 cystathionine gamma-lyase activity was measured (UniProt CATALYTIC ACTIVITY, ECO:0000269 PubMed:19955263), although its main role is L-cysteine desulfhydration. - go_id: GO:0019808 label: polyamine binding aspect: MF annotations: - UniProtKB:D8T634 (Selaginella, IEA) - UniProtKB:D8T7W8 (Selaginella, IEA) - UniProtKB:F4I9D4 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR001188 (PotD/PotF periplasmic binding protein) verdict: UNCERTAIN reason: ENF2 and the Selaginella homologs are plastid PotD-like proteins whose polyamine binding has not been tested; the mapping assumes bacterial PotD function. A ligand-binding assay would settle it. - go_id: GO:1902004 label: positive regulation of amyloid-beta formation aspect: BP annotations: - UniProtKB:Q9ZQI2 (Arabidopsis, ISS) mechanism: ISS (UniProt) from UniProtKB:P42574 human caspase-3 verdict: ANNOTATION_WRONG reason: 'Symbol collision: the source is human CASP3 (caspase-3), while Q9ZQI2 is Arabidopsis CASP3, a Casparian strip membrane domain protein with no relation to caspases. The ISS should be withdrawn; other rows from the same source on this entry deserve checking.' - go_id: GO:0103026 label: fructose-1-phosphatase activity aspect: MF annotations: - UniProtKB:Q9ZVJ5 (Arabidopsis, IEA) mechanism: IEA RHEA:35603 mapping verdict: FLAG_FAILS reason: SGPP fructose-1-phosphate hydrolysis was measured (UniProt CATALYTIC ACTIVITY, ECO:0000269 PubMed:23179445) as part of its broad phosphosugar specificity. - go_id: GO:0071396 label: cellular response to lipid aspect: BP annotations: - UniProtKB:O80920 (Arabidopsis, IEA) - UniProtKB:Q8S8E3 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00027803 verdict: TRUE_BUT_GENERAL reason: PYL4/PYL6 are ABA receptors; ABA counts as a lipid in ChEBI, so the term is true but the ABA signalling term fits. replacement: GO:0009738 abscisic acid-activated signaling pathway - go_id: GO:0031402 label: sodium ion binding aspect: MF annotations: - UniProtKB:Q9S795 (Arabidopsis, ISS) - UniProtKB:Q9STS1 (Arabidopsis, ISS) mechanism: ISS (UniProt) PMID:20026072 from pea AMADH1 UniProtKB:Q8VWZ1 verdict: FLAG_FAILS reason: ALDH10 aminoaldehyde dehydrogenases bind a structural monovalent cation seen in the pea AMADH structure; the ISS to the close Arabidopsis orthologs is reasonable. - go_id: GO:0110153 label: RNA NAD-cap (NMN-forming) hydrolase activity aspect: MF annotations: - UniProtKB:Q94A82 (Arabidopsis, IEA/ISS) mechanism: IEA RHEA:60876; ISS from mouse Nudt12 UniProtKB:Q9DCN1 verdict: FLAG_FAILS reason: NUDT19 removes NAD caps from mRNAs (UniProt FUNCTION); mappings sound. - go_id: GO:0017003 label: protein-heme linkage aspect: BP annotations: - UniProtKB:Q96326 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR004329 + IPR036127 (CcmE) verdict: FLAG_FAILS reason: CcmE covalently binds heme as the System I chaperone, and plant mitochondrial CCME binds heme (UniProt, PubMed:11069919). Note IPR036127 also maps 'plasma membrane', wrong for this mitochondrial protein. - go_id: GO:0015851 label: nucleobase transport aspect: BP annotations: - UniProtKB:D8RGZ2 (Selaginella, IEA) - UniProtKB:D8S5K2 (Selaginella, IEA) - UniProtKB:Q9LZD0 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015205 nucleobase TM transporter activity verdict: FLAG_FAILS reason: NCS1 is a nucleobase-proton symporter (UniProt FUNCTION); mechanical inference. - go_id: GO:0008287 label: protein serine/threonine phosphatase complex aspect: CC annotations: - UniProtKB:O04719 (Arabidopsis, TAS) - UniProtKB:P49597 (Arabidopsis, TAS) mechanism: TAS (TIGR) PMID:9869399 verdict: UNCERTAIN reason: ABI1/ABI2 are PP2Cs that act as monomers or in receptor-bound inhibited complexes; the 1998 statement likely meant the activity. Consistent with the repo ABI1 review (UNDECIDED); the full text would settle the intended claim. replacement: GO:0004722 protein serine/threonine phosphatase activity - go_id: GO:0070127 label: tRNA aminoacylation for mitochondrial protein translation aspect: BP annotations: - UniProtKB:F4I4Z2 (Arabidopsis, IEA) - UniProtKB:P36428 (Arabidopsis, IEA) mechanism: IEA UniRule UR000375824 (HAMAP Ala_tRNA_synth_euk) verdict: FLAG_FAILS reason: Arabidopsis AlaRS is dual-targeted to cytosol and mitochondria, so mitochondrial aminoacylation is right. - go_id: GO:0016589 label: NURF complex aspect: CC annotations: - UniProtKB:D8RE40 (Selaginella, IEA) - UniProtKB:D8STZ1 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR038028 (BPTF) verdict: FLAG_FAILS reason: PANTHER also places D8RE40/D8STZ1 in the BPTF family (no Arabidopsis members), so Selaginella appears to keep a NURF301 homolog lost in angiosperms; plausible rare biology. - go_id: GO:0016469 label: proton-transporting two-sector ATPase complex aspect: CC annotations: - UniProtKB:O82628 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:11004467 verdict: TRUE_BUT_GENERAL reason: VHA-G1 is a V1-sector subunit of the vacuolar ATPase; the two-sector complex term is a correct parent. replacement: GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain - go_id: GO:0019211 label: phosphatase activator activity aspect: MF annotations: - UniProtKB:D8SYB5 (Selaginella, IEA) - UniProtKB:D8T749 (Selaginella, IEA) - UniProtKB:F4JJ86 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR004327 + IPR037218 (PTPA) verdict: FLAG_FAILS reason: PTPA proteins activate PP2A in all eukaryotes; mapping sound. - go_id: GO:0019373 label: epoxygenase P450 pathway aspect: BP annotations: - UniProtKB:Q96242 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:8378325 (flax allene oxide synthase) verdict: ANNOTATION_WRONG reason: CYP74A is allene oxide synthase in jasmonate biosynthesis (UniProt FUNCTION); the epoxygenase P450 pathway is arachidonic acid to EETs in animals. The allene oxide is an epoxide, which probably explains the mis-choice. replacement: GO:0009695 jasmonic acid biosynthetic process - go_id: GO:0061513 label: glucose 6-phosphate:phosphate antiporter activity aspect: MF annotations: - UniProtKB:O23596 (Arabidopsis, IEA) - UniProtKB:Q9SA71 (Arabidopsis, IEA) - UniProtKB:Q9SL56 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR044740 (SLC37A1/SLC37A2) verdict: UNCERTAIN reason: The three Arabidopsis members are putative glycerol-3-phosphate permeases (G3Pp3/4/5) of the OPA family whose characterized paralog transports G3P; the family named for vertebrate G6P antiporters may overreach for plants. A transport assay would settle it. replacement: GO:0015169 glycerol-3-phosphate transmembrane transporter activity - go_id: GO:0015793 label: glycerol transmembrane transport aspect: BP annotations: - UniProtKB:Q8VZ80 (Arabidopsis, IEA) - UniProtKB:Q9SAI4 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0015168 glycerol TM transporter activity verdict: FLAG_FAILS reason: PLT5 and NIP6;1 transport glycerol (UniProt FUNCTION, NIP6;1 PubMed:16363796); mechanical inference. - go_id: GO:0032559 label: adenyl ribonucleotide binding aspect: MF annotations: - UniProtKB:C7B2E9 (Selaginella, IEA) - UniProtKB:F4IMB5 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR033732 (F1 alpha nucleotide-binding domain) verdict: TRUE_BUT_GENERAL reason: ATP synthase alpha binds ATP/ADP; the grouping term is a correct parent. F4IMB5 (At2g07698, 777 aa) is an unusual ATP synthase alpha copy whose gene model deserves checking. replacement: GO:0005524 ATP binding - go_id: GO:0006851 label: mitochondrial calcium ion transmembrane transport aspect: BP annotations: - UniProtKB:D8RGN7 (Selaginella, IEA) - UniProtKB:D8S591 (Selaginella, IEA) - UniProtKB:Q9SZ45 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR039800 (MICU) verdict: FLAG_FAILS reason: AtMICU regulates mitochondrial Ca2+ uptake through the uniporter (UniProt FUNCTION, PubMed:26530087); mapping sound. - go_id: GO:0051180 label: vitamin transport aspect: BP annotations: - UniProtKB:D8RLU9 (Selaginella, IEA) - UniProtKB:D8RNC5 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR002666 (reduced folate carrier) verdict: FLAG_FAILS reason: SLC19/RFC-family members transport folates or thiamine; Selaginella keeps homologs absent from Arabidopsis. - go_id: GO:0071027 label: nuclear RNA surveillance aspect: BP annotations: - UniProtKB:D8SCD7 (Selaginella, IEA) - UniProtKB:D8SGL5 (Selaginella, IEA) - UniProtKB:Q9SP08 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00027040 verdict: FLAG_FAILS reason: RRP41 is a core RNA exosome subunit, which carries out nuclear RNA surveillance in all eukaryotes. - go_id: GO:0015757 label: galactose transmembrane transport aspect: BP annotations: - UniProtKB:Q8GW61 (Arabidopsis, IEA) - UniProtKB:Q8VZ80 (Arabidopsis, IEA) - UniProtKB:Q9LT15 (Arabidopsis, IEA) mechanism: IEA GOC inference from GO:0005354 galactose TM transporter activity verdict: FLAG_FAILS reason: STP10, STP14 and PLT5 transport galactose (UniProt FUNCTION); mechanical inference. - go_id: GO:0032482 label: Rab protein signal transduction aspect: BP annotations: - UniProtKB:D8QUM7 (Selaginella, IEA) - UniProtKB:D8T1E0 (Selaginella, IEA) mechanism: IEA InterPro2GO InterPro:IPR041833 (Rab21) verdict: FLAG_FAILS reason: Generic signalling term attached to Rab subfamilies; true for a Rab21 GTPase. - go_id: GO:0006884 label: cell volume homeostasis aspect: BP annotations: - UniProtKB:D8R326 (Selaginella, IEA) - UniProtKB:Q9LVA7 (Arabidopsis, IEA) mechanism: IEA InterPro2GO InterPro:IPR003521 (ICln) verdict: UNCERTAIN reason: The ICln volume/chloride-current role comes from contested animal work, and its conserved role is in the methylosome for snRNP assembly; no plant volume phenotype is reported. Evidence for a plant ICln volume role would settle it; otherwise prefer the snRNP assembly mapping. - go_id: GO:0015931 label: nucleobase-containing compound transport aspect: BP annotations: - UniProtKB:D8RD67 (Selaginella, IEA) - UniProtKB:D8RFA2 (Selaginella, IEA) mechanism: IEA GOC inference from GO:0005338 nucleotide-sugar TM transporter activity verdict: TRUE_BUT_GENERAL reason: Same mechanism as GO:1901264; nucleotide sugars are nucleobase-containing, so true but general. replacement: GO:0015780 nucleotide-sugar transmembrane transport - go_id: GO:0004466 label: long-chain fatty acyl-CoA dehydrogenase activity aspect: MF annotations: - UniProtKB:D8S3D8 (Selaginella, IEA) - UniProtKB:D8S7U7 (Selaginella, IEA) mechanism: IEA EC:1.3.8.8 mapping verdict: UNCERTAIN reason: D8S3D8/D8S7U7 are ACAD11-like (APH kinase plus ACAD domains); plant fatty acid beta-oxidation is mainly peroxisomal via acyl-CoA oxidases, and the EC on these unreviewed entries is rule-derived. A substrate assay would settle it. - go_id: GO:0016461 label: unconventional myosin complex aspect: CC annotations: - UniProtKB:F4IRU3 (Arabidopsis, ISS) mechanism: ISS (TAIR) PMID:7811972 verdict: FLAG_FAILS reason: Myosin XI is a non-myosin-II class, so 'unconventional myosin complex' holds; plants have no myosin II at all. - group: plants_experimental terms: 358 entry_count: 370 verdicts: ANNOTATION_WRONG: 23 CONSTRAINT_QUESTIONABLE: 2 DEFER_TO_CURATOR: 277 FLAG_FAILS: 59 UNCERTAIN: 9 summary: '358 terms in 370 entries: ANNOTATION_WRONG 23, CONSTRAINT_QUESTIONABLE 2, FLAG_FAILS 59, TRUE_BUT_GENERAL 0, DEFER_TO_CURATOR 277, UNCERTAIN 9. Most flags are real plant biology at low curation density: plant enzymes, or IBA nodes seeded by the Arabidopsis gene itself. The wrong calls are mostly term-choice slips on experimental rows. Three kinds stand out: homonyms (cytokine for cytokinin x2, seed-coat "endothelium", 2'',3''-cAMP filed as 3'',5''-cAMP, synthase for synthetase, Fe/ascorbate oxidase); animal structures (focal adhesion, perinuclear theca, anchoring junction); and apoptosis/tissue-regeneration terms that break existing constraints. A systematic IEA source is the sl2go mapping of SL-0038 "Cell junction" to GO:0070161 anchoring junction, which lands on plasmodesmal proteins.' fetched_pmids: - PMID:22171001 - PMID:16832061 - PMID:19704797 - PMID:16361528 - PMID:34504049 - PMID:23911125 - PMID:37979582 - PMID:29702752 - PMID:30156702 - PMID:19941015 - PMID:35605192 - PMID:28724620 - PMID:15020741 - PMID:22233288 - PMID:33615694 - PMID:15677481 - PMID:8883383 - PMID:21967323 - PMID:24800789 - PMID:11432958 entries: - go_id: GO:0032993 label: protein-DNA complex aspect: CC annotations: - UniProtKB:O24646 HY5 (Arabidopsis, IMP) mechanism: IMP PMID:17001643 (CAFA) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from CAFA on HY5 rest on full text not read here. - go_id: GO:0030054 label: cell junction aspect: CC annotations: - UniProtKB:Q8LPJ1 CKL6 (Arabidopsis, IDA) mechanism: IDA PMID:19941015 (UniProt) verdict: DEFER_TO_CURATOR reason: Cell junction includes plasmodesmata; the CKL6 IDA is consistent with its UniProt plasmodesmal location. - go_id: GO:0043065 label: positive regulation of apoptotic process aspect: BP annotations: - UniProtKB:Q9LSF1 OXI1 (Arabidopsis, IMP) mechanism: IMP PMID:31123095 (TAIR) verdict: ANNOTATION_WRONG reason: Breaks the GO constraint (apoptotic process only in Opisthokonta); OXI1 promotes plant programmed cell death, for which GO has a plant-applicable term. replacement: GO:0043068 positive regulation of programmed cell death - go_id: GO:0030427 label: site of polarized growth aspect: CC annotations: - UniProtKB:Q38912 ARAC3 (Arabidopsis, IDA) mechanism: IDA PMID:11387211 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ARAC3 rest on full text not read here. - go_id: GO:0043410 label: positive regulation of MAPK cascade aspect: BP annotations: - UniProtKB:Q1PDV6 PBL27 (Arabidopsis, IMP) mechanism: IMP PMID:24750441 (GO_Central) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from GO_Central on PBL27 rest on full text not read here. - go_id: GO:0070161 label: anchoring junction aspect: CC annotations: - UniProtKB:Q8LPJ1 CKL6 (Arabidopsis, EXP/IEA) mechanism: IEA UniProtKB-SubCell:SL-0038 (sl2go maps 'Cell junction' to anchoring junction); EXP PMID:19941015 (UniProt) carries the same term verdict: ANNOTATION_WRONG reason: CKL6/PAPK1 sits at plasmodesmata and in vesicles at the cell periphery, not in an anchoring junction (a cytoskeleton-to-neighbour or -matrix attachment, which plants do not build). The sl2go file maps SL-0038 "Cell junction" to GO:0070161, so every plant protein with UniProt location "Cell junction, plasmodesma" inherits anchoring junction; the mapping should target GO:0030054 cell junction. replacement: GO:0009506 plasmodesma (GO:0030054 cell junction is already on CKL6 by IDA) - go_id: GO:0043235 label: signaling receptor complex aspect: CC annotations: - UniProtKB:Q9SJV5 TATC (Arabidopsis, IDA) mechanism: IDA PMID:19207210 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on TATC rest on full text not read here. - go_id: GO:0061629 label: RNA polymerase II-specific DNA-binding transcription factor binding aspect: MF annotations: - UniProtKB:O81834 BBX28 (Arabidopsis, IPI) mechanism: IPI PMID:30099385 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on BBX28 rest on full text not read here. - go_id: GO:0043066 label: negative regulation of apoptotic process aspect: BP annotations: - UniProtKB:D8SSK8 (Selaginella, IBA) - UniProtKB:Q9C901 At3g06610 (Arabidopsis, IBA) - UniProtKB:Q9SNC6 PUB13 (Arabidopsis, IMP) mechanism: IBA PANTHER:PTN001580765; IMP PMID:22383540 (CACAO) verdict: ANNOTATION_WRONG reason: Breaks the Opisthokonta-only constraint. The IBA comes from PTN001580765 seeded only by human HYPK (Q9NX55), whose anti-apoptotic role is animal; the PUB13 IMP describes suppression of plant cell death. Plant rows belong on the programmed-cell-death parent. replacement: GO:0043069 negative regulation of programmed cell death - go_id: GO:0005125 label: cytokine activity aspect: MF annotations: - UniProtKB:P33154 At2g14610 (Arabidopsis, IMP) mechanism: IMP PMID:37542077 (TAIR) verdict: DEFER_TO_CURATOR reason: The paper shows PR-1 is cleaved into the CAPE9 peptide for systemic immunity (a phytocytokine). The cytokine definition is not animal-restricted, but plant peptide signals usually go to hormone or receptor-ligand activity terms, so the curator should confirm the choice. - go_id: GO:0099617 label: matrix side of mitochondrial inner membrane aspect: CC annotations: - UniProtKB:Q1JPL4 NDB1 (Arabidopsis, IDA) mechanism: IDA PMID:16258072 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on NDB1 rest on full text not read here. - go_id: GO:0032541 label: cortical endoplasmic reticulum aspect: CC annotations: - UniProtKB:O22227 MIZ1 (Arabidopsis, IDA) - UniProtKB:Q9SKR2 SYT1 (Arabidopsis, IDA) mechanism: IDA PMID:22285304 (TAIR); IDA PMID:25792253 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on MIZ1, SYT1 rest on full text not read here. - go_id: GO:0043200 label: response to amino acid aspect: BP annotations: - UniProtKB:O24495 GLX2-1 (Arabidopsis, IMP) mechanism: IMP PMID:24760003 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on GLX2-1 rest on full text not read here. - go_id: GO:0042826 label: histone deacetylase binding aspect: MF annotations: - UniProtKB:O22130 AHL22 (Arabidopsis, IPI) mechanism: IPI PMID:22442143 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from UniProt on AHL22 rest on full text not read here. - go_id: GO:0051701 label: biological process involved in interaction with host aspect: BP annotations: - UniProtKB:Q0PCS3 CHR25 (Arabidopsis, IPI) mechanism: IPI PMID:22171001 (UniProt) verdict: ANNOTATION_WRONG reason: The term is for the symbiont's side of an interaction; RAD54 is the host (plant) factor bound by geminivirus Rep (with_from P36279 ToLCV Rep, Q9YPS2 MYMV Rep). A host protein needs the host-side or virus-replication term. replacement: GO:0045070 positive regulation of viral genome replication (or GO:0051702 biological process involved in interaction with symbiont) supported_by: - reference_id: PMID:22171001 supporting_text: We have identified a host factor, RAD54, in a screen for Rep-interacting partners - go_id: GO:0035264 label: multicellular organism growth aspect: BP annotations: - UniProtKB:Q96289 ZAT10 (Arabidopsis, IMP) mechanism: IMP PMID:15333755 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on ZAT10 rest on full text not read here. - go_id: GO:0006279 label: premeiotic DNA replication aspect: BP annotations: - UniProtKB:Q9LSG6 CDC45 (Arabidopsis, IMP) mechanism: IMP PMID:14660803 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CDC45 rest on full text not read here. - go_id: GO:0042593 label: glucose homeostasis aspect: BP annotations: - UniProtKB:Q9FRL3 At1g75220 (Arabidopsis, IMP) mechanism: IMP PMID:21984725 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At1g75220 rest on full text not read here. - go_id: GO:0007026 label: negative regulation of microtubule depolymerization aspect: BP annotations: - UniProtKB:Q8RWY6 CLASP (Arabidopsis, IMP) mechanism: IMP PMID:17873093 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on CLASP rest on full text not read here. - go_id: GO:0031508 label: pericentric heterochromatin formation aspect: BP annotations: - UniProtKB:Q8VYZ0 ORTH2 (Arabidopsis, IMP) mechanism: IMP PMID:17242155 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on ORTH2 rest on full text not read here. - go_id: GO:0097038 label: perinuclear endoplasmic reticulum aspect: CC annotations: - UniProtKB:B3H4Y2 STMP3 (Arabidopsis, IDA) mechanism: IDA PMID:31001913 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on STMP3 rest on full text not read here. - go_id: GO:1903432 label: regulation of TORC1 signaling aspect: BP annotations: - UniProtKB:Q940X9 LARP1A (Arabidopsis, IMP) mechanism: IMP PMID:33054972 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on LARP1A rest on full text not read here. - go_id: GO:0031520 label: plasma membrane of cell tip aspect: CC annotations: - UniProtKB:Q9C5G5 SAC7 (Arabidopsis, IDA) mechanism: IDA PMID:18281508 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SAC7 rest on full text not read here. - go_id: GO:0045184 label: establishment of protein localization aspect: BP annotations: - UniProtKB:C0LGQ5 GSO1 (Arabidopsis, IMP) mechanism: IMP PMID:25233277 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on GSO1 rest on full text not read here. - go_id: GO:0071474 label: cellular hyperosmotic response aspect: BP annotations: - UniProtKB:Q9XEA1 OSCA1 (Arabidopsis, IDA/IMP) mechanism: IDA PMID:25162526 (UniProt); IMP PMID:25162526 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on OSCA1 rest on full text not read here. - go_id: GO:0015087 label: cobalt ion transmembrane transporter activity aspect: MF annotations: - UniProtKB:F4KGN5 IREG2 (Arabidopsis, IMP) mechanism: IMP PMID:19861554 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on IREG2 rest on full text not read here. - go_id: GO:1903785 label: L-valine transmembrane transport aspect: BP annotations: - UniProtKB:Q84MA5 CAT1 (Arabidopsis, IDA) mechanism: IDA PMID:8618839 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CAT1 rest on full text not read here. - go_id: GO:0004622 label: phosphatidylcholine lysophospholipase A1 activity aspect: MF annotations: - UniProtKB:Q9C942 CSE (Arabidopsis, IDA) mechanism: IDA PMID:20345607 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CSE rest on full text not read here. - go_id: GO:1902533 label: positive regulation of intracellular signal transduction aspect: BP annotations: - UniProtKB:Q7XJT7 BSK12 (Arabidopsis, IGI) mechanism: IGI PMID:19286558 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on BSK12 rest on full text not read here. - go_id: GO:0000182 label: rDNA binding aspect: MF annotations: - UniProtKB:O23215 PBRP1 (Arabidopsis, IDA) mechanism: IDA PMID:18668124 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PBRP1 rest on full text not read here. - go_id: GO:0042149 label: cellular response to glucose starvation aspect: BP annotations: - UniProtKB:D8T658 (Selaginella, IBA) - UniProtKB:D8T7U4 (Selaginella, IBA) - UniProtKB:Q944A6 SNF4 (Arabidopsis, IBA/IDA) mechanism: IBA PANTHER:PTN008551371; IDA PMID:10929106 (TAIR) verdict: FLAG_FAILS reason: SnRK1 regulatory subunit SNF4 (AKINbetagamma); IBA PTN008551371 seeded by SNF4 itself; glucose starvation signalling is conserved. - go_id: GO:1990023 label: mitotic spindle midzone aspect: CC annotations: - UniProtKB:F4ICA0 KIN8A (Arabidopsis, IBA) - UniProtKB:Q8LEG3 MAP65-2 (Arabidopsis, IDA) mechanism: IBA PANTHER:PTN000649974; IDA PMID:19060108 (TAIR) verdict: FLAG_FAILS reason: Kinesin-8 IBA (PTN000649974) plus IDA; plant mitotic spindles have a midzone in anaphase, rare only by curation density. - go_id: GO:0006824 label: cobalt ion transport aspect: BP annotations: - UniProtKB:F4KGN5 IREG2 (Arabidopsis, IMP) - UniProtKB:O80905 IREG1 (Arabidopsis, IMP) mechanism: IMP PMID:19861554 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on IREG1, IREG2 rest on full text not read here. - go_id: GO:0005796 label: Golgi lumen aspect: CC annotations: - UniProtKB:Q9M9N9 AXY9 (Arabidopsis, IDA/IPI) mechanism: IDA PMID:25681330 (TAIR); IPI PMID:25681330 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IPI row(s) from TAIR on AXY9 rest on full text not read here. - go_id: GO:0045471 label: response to ethanol aspect: BP annotations: - UniProtKB:Q8S926 ATG8E (Arabidopsis, IDA) mechanism: IDA PMID:33028029 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ATG8E rest on full text not read here. - go_id: GO:0045596 label: negative regulation of cell differentiation aspect: BP annotations: - UniProtKB:Q9MA75 VIP1 (Arabidopsis, IDA) mechanism: IDA PMID:15108305 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on VIP1 rest on full text not read here. - go_id: GO:0140311 label: protein sequestering activity aspect: MF annotations: - UniProtKB:Q9LSZ8 MQM1.5 (Arabidopsis, IDA) mechanism: IDA PMID:42203875 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on MQM1.5 rest on full text not read here. - go_id: GO:0070888 label: E-box binding aspect: MF annotations: - UniProtKB:Q9LND0 BHLH89 (Arabidopsis, IPI) mechanism: IPI PMID:33393464 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on BHLH89 rest on full text not read here. - go_id: GO:0016050 label: vesicle organization aspect: BP annotations: - UniProtKB:O80796 VIPP1 (Arabidopsis, IMP) mechanism: IMP PMID:11274447 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on VIPP1 rest on full text not read here. - go_id: GO:0015871 label: choline transport aspect: BP annotations: - UniProtKB:Q94AN2 CHER1 (Arabidopsis, IDA/IMP) mechanism: IDA PMID:25008948 (TAIR); IMP PMID:27743414 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on CHER1 rest on full text not read here. - go_id: GO:0005304 label: L-valine transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q84MA5 CAT1 (Arabidopsis, IDA) mechanism: IDA PMID:8618839 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CAT1 rest on full text not read here. - go_id: GO:0140374 label: antiviral innate immune response aspect: BP annotations: - UniProtKB:Q93VT9 RPL10A (Arabidopsis, IMP) - UniProtKB:Q9LFS4 CIK5 (Arabidopsis, IMP) mechanism: IMP PMID:19112492 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on CIK5, RPL10A rest on full text not read here. - go_id: GO:0034644 label: cellular response to UV aspect: BP annotations: - UniProtKB:Q9C7X0 ADR2 (Arabidopsis, IMP) mechanism: IMP PMID:25656510 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on ADR2 rest on full text not read here. - go_id: GO:0048312 label: intracellular distribution of mitochondria aspect: BP annotations: - UniProtKB:F4J5S1 FMT (Arabidopsis, IMP) mechanism: IMP PMID:14617080 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on FMT rest on full text not read here. - go_id: GO:0015578 label: mannose transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9LT15 STP10 (Arabidopsis, IDA) mechanism: IDA PMID:26893494 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on STP10 rest on full text not read here. - go_id: GO:0001784 label: phosphotyrosine residue binding aspect: MF annotations: - UniProtKB:Q9LJK1 FUT11 (Arabidopsis, IDA) mechanism: IDA PMID:41577690 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on FUT11 rest on full text not read here. - go_id: GO:0042030 label: ATPase inhibitor activity aspect: MF annotations: - UniProtKB:Q9SUA6 CBL7 (Arabidopsis, IDA) mechanism: IDA PMID:30962395 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CBL7 rest on full text not read here. - go_id: GO:0007006 label: mitochondrial membrane organization aspect: BP annotations: - UniProtKB:Q9LVA9 GCD1 (Arabidopsis, IMP) mechanism: IMP PMID:23085019 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on GCD1 rest on full text not read here. - go_id: GO:0016562 label: protein import into peroxisome matrix, receptor recycling aspect: BP annotations: - UniProtKB:Q8LGF7 PEX4 (Arabidopsis, IMP) mechanism: IMP PMID:35595097 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PEX4 rest on full text not read here. - go_id: GO:0032042 label: mitochondrial DNA metabolic process aspect: BP annotations: - UniProtKB:Q84LK0 MSH1 (Arabidopsis, IMP) mechanism: IMP PMID:12730382 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on MSH1 rest on full text not read here. - go_id: GO:0034097 label: response to cytokine aspect: BP annotations: - UniProtKB:P0DO11 FLZ17 (Arabidopsis, IEP) mechanism: IEP PMID:16832061 (UniProt) verdict: ANNOTATION_WRONG reason: 'Cytokine/cytokinin slip: the cited paper is a cytokinin-response study and never mentions cytokines, which plants do not make. FLZ17 (At1g53885) should carry the cytokinin term.' replacement: GO:0009735 response to cytokinin supported_by: - reference_id: PMID:16832061 supporting_text: A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. - go_id: GO:0009008 label: DNA-methyltransferase activity aspect: MF annotations: - UniProtKB:Q8LFA9 At1g19340 (Arabidopsis, IDA) - UniProtKB:Q9M548 DRM2 (Arabidopsis, IGI/IMP) mechanism: IDA PMID:37944704 (TAIR); IGI PMID:17239600 (TAIR); IMP PMID:21212233 (CACAO) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IGI/IMP row(s) from CACAO/TAIR on At1g19340, DRM2 rest on full text not read here. - go_id: GO:0008301 label: DNA binding, bending aspect: MF annotations: - UniProtKB:Q9C7B1 TRP3 (Arabidopsis, IDA) - UniProtKB:Q9SNB9 TRP2 (Arabidopsis, IDA) mechanism: IDA PMID:15688221 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on TRP2, TRP3 rest on full text not read here. - go_id: GO:0007204 label: positive regulation of cytosolic calcium ion concentration aspect: BP annotations: - UniProtKB:F4I5N6 RIC3 (Arabidopsis, IMP) - UniProtKB:Q1ECR9 RALFL8 (Arabidopsis, EXP) mechanism: IMP PMID:15824136 (TAIR); EXP PMID:31004454 (DisProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; EXP/IMP row(s) from DisProt/TAIR on RALFL8, RIC3 rest on full text not read here. - go_id: GO:0034501 label: protein localization to kinetochore aspect: BP annotations: - UniProtKB:F4JT58 EMB3006 (Arabidopsis, IPI) mechanism: IPI PMID:34850467 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on EMB3006 rest on full text not read here. - go_id: GO:0034455 label: t-UTP complex aspect: CC annotations: - UniProtKB:F4JWG2 NUGWD1 (Arabidopsis, IPI) mechanism: IPI PMID:26555280 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on NUGWD1 rest on full text not read here. - go_id: GO:2000026 label: regulation of multicellular organismal development aspect: BP annotations: - UniProtKB:O22446 HDA19 (Arabidopsis, IMP) mechanism: IMP PMID:11134508 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on HDA19 rest on full text not read here. - go_id: GO:0006805 label: xenobiotic metabolic process aspect: BP annotations: - UniProtKB:Q9M0G0 GGT3 (Arabidopsis, IEP) - UniProtKB:Q9M156 UGT72B1 (Arabidopsis, IMP) mechanism: IEP PMID:17316176 (TAIR); IMP PMID:15860014 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP/IMP row(s) from TAIR on GGT3, UGT72B1 rest on full text not read here. - go_id: GO:0001221 label: transcription coregulator binding aspect: MF annotations: - UniProtKB:O82132 DREB2A (Arabidopsis, EXP) mechanism: EXP PMID:27881680 (DisProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; EXP row(s) from DisProt on DREB2A rest on full text not read here. - go_id: GO:1902895 label: positive regulation of miRNA transcription aspect: BP annotations: - UniProtKB:F4KF35 MVP7.5 (Arabidopsis, IMP) mechanism: IMP PMID:35260568 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on MVP7.5 rest on full text not read here. - go_id: GO:0042834 label: peptidoglycan binding aspect: MF annotations: - UniProtKB:Q6NPN4 LYM3 (Arabidopsis, IBA/IDA) - UniProtKB:Q93ZH0 LYM1 (Arabidopsis, IBA/IDA) mechanism: IBA PANTHER:PTN001915799; IDA PMID:22106285 (TAIR) verdict: FLAG_FAILS reason: LYM1/LYM3 LysM proteins bind bacterial peptidoglycan (IDA), and the IBA node is seeded by them. - go_id: GO:0005272 label: sodium channel activity aspect: MF annotations: - UniProtKB:Q9M8W7 GLR1.1 (Arabidopsis, IDA) mechanism: IDA PMID:18625242 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on GLR1.1 rest on full text not read here. - go_id: GO:0098586 label: cellular response to virus aspect: BP annotations: - UniProtKB:Q9FI46 CRL (Arabidopsis, IDA) mechanism: IDA PMID:19840398 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CRL rest on full text not read here. - go_id: GO:0140474 label: mitochondrion-endoplasmic reticulum membrane tether activity aspect: MF annotations: - UniProtKB:F4I8P4 YUP8H12.12 (Arabidopsis, IPI) mechanism: IPI PMID:36163196 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on YUP8H12.12 rest on full text not read here. - go_id: GO:0016805 label: dipeptidase activity aspect: MF annotations: - UniProtKB:P30184 LAP1 (Arabidopsis, IDA) - UniProtKB:Q8RX72 LAP3 (Arabidopsis, IDA) mechanism: IDA PMID:25716890 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on LAP1, LAP3 rest on full text not read here. - go_id: GO:0071345 label: cellular response to cytokine stimulus aspect: BP annotations: - UniProtKB:P48000 KNAT3 (Arabidopsis, IDA) mechanism: IDA PMID:19704797 (TAIR) verdict: ANNOTATION_WRONG reason: 'Same cytokine/cytokinin slip: the paper reports that cytokinin represses the KNAT3 promoter; the word cytokine does not occur in it.' replacement: GO:0009735 response to cytokinin (GO:0071368 cellular response to cytokinin stimulus if the curator wants the cellular form) supported_by: - reference_id: PMID:19704797 supporting_text: cytokinin drastically decreased the activity of the KNAT3 promoter - go_id: GO:0071469 label: cellular response to alkaline pH aspect: BP annotations: - UniProtKB:Q940Y5 PIN7 (Arabidopsis, IDA) - UniProtKB:Q9S7Z8 PIN3 (Arabidopsis, IDA) mechanism: IDA PMID:36582637 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PIN3, PIN7 rest on full text not read here. - go_id: GO:2000144 label: positive regulation of DNA-templated transcription initiation aspect: BP annotations: - UniProtKB:Q94C37 HDG2 (Arabidopsis, IDA) mechanism: IDA PMID:33631797 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on HDG2 rest on full text not read here. - go_id: GO:0001933 label: negative regulation of protein phosphorylation aspect: BP annotations: - UniProtKB:Q9FNP4 PIA2 (Arabidopsis, IMP) mechanism: IMP PMID:27143545 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PIA2 rest on full text not read here. - go_id: GO:0140268 label: endoplasmic reticulum-plasma membrane contact site aspect: CC annotations: - UniProtKB:Q7XA06 SYT3 (Arabidopsis, IDA) - UniProtKB:Q9SKR2 SYT1 (Arabidopsis, IDA) mechanism: IDA PMID:33944955 (TAIR); IDA PMID:30126867 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SYT1, SYT3 rest on full text not read here. - go_id: GO:0051292 label: nuclear pore complex assembly aspect: BP annotations: - UniProtKB:Q9LN10 At1g07970 (Arabidopsis, IPI) mechanism: IPI PMID:39890949 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on At1g07970 rest on full text not read here. - go_id: GO:0042175 label: nuclear outer membrane-endoplasmic reticulum membrane network aspect: CC annotations: - UniProtKB:D8R2Z3 (Selaginella, IBA) - UniProtKB:Q9LE45 SUB1 (Arabidopsis, IDA) mechanism: IBA PANTHER:PTN001256837; IDA PMID:11161203 (TAIR) verdict: FLAG_FAILS reason: ER/nuclear outer membrane network location is conserved; IBA node PTN001256837 and Arabidopsis IDA agree. - go_id: GO:0006799 label: polyphosphate biosynthetic process aspect: BP annotations: - UniProtKB:Q8S403 PHO1 (Arabidopsis, IMP) mechanism: IMP PMID:27080106 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PHO1 rest on full text not read here. - go_id: GO:0006171 label: cAMP biosynthetic process aspect: BP annotations: - UniProtKB:F4HT77 RBA1 (Arabidopsis, IMP) mechanism: IMP PMID:35597242 (UniProt) verdict: ANNOTATION_WRONG reason: GO:0006171 is 3',5'-cAMP. The RBA1 TIR domain makes 2',3'-cAMP/cGMP by hydrolysing RNA/DNA, a different molecule; the same paper separates 2',3'- from 3',5'-cNMP enzymology. No 2',3'-cAMP biosynthesis term exists (ontology gap). supported_by: - reference_id: PMID:35597242 supporting_text: act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA - go_id: GO:0031397 label: negative regulation of protein ubiquitination aspect: BP annotations: - UniProtKB:F4HVZ5 CSU2 (Arabidopsis, IDA) mechanism: IDA PMID:26714275 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CSU2 rest on full text not read here. - go_id: GO:0033558 label: protein lysine deacetylase activity aspect: MF annotations: - UniProtKB:Q941D6 HDA14 (Arabidopsis, IDA) mechanism: IDA PMID:29061669 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on HDA14 rest on full text not read here. - go_id: GO:7770062 label: vesicle membrane tethering activity aspect: MF annotations: - UniProtKB:F4HUA9 At1g07985 (Arabidopsis, IDA) - UniProtKB:F4K2W9 MAB16.4 (Arabidopsis, IDA) - UniProtKB:Q9LVY8 MAB16.4 (Arabidopsis, IDA) mechanism: IDA PMID:42176019 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on At1g07985, MAB16.4 rest on full text not read here. - go_id: GO:0046487 label: glyoxylate metabolic process aspect: BP annotations: - UniProtKB:Q9FMN0 SCP2 (Arabidopsis, IMP) mechanism: IMP PMID:18687588 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on SCP2 rest on full text not read here. - go_id: GO:0015970 label: guanosine tetraphosphate biosynthetic process aspect: BP annotations: - UniProtKB:Q9SYH1 RSH3 (Arabidopsis, IGI/IMP) mechanism: IGI PMID:26908759 (TAIR); IMP PMID:26908759 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IMP row(s) from TAIR on RSH3 rest on full text not read here. - go_id: GO:0015269 label: calcium-activated potassium channel activity aspect: MF annotations: - UniProtKB:Q8LBL1 TPK1 (Arabidopsis, IDA) mechanism: IDA PMID:9184204 (TIGR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TIGR on TPK1 rest on full text not read here. - go_id: GO:2000637 label: positive regulation of miRNA-mediated gene silencing aspect: BP annotations: - UniProtKB:Q8L7S8 RH3 (Arabidopsis, IMP) mechanism: IMP PMID:40000658 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on RH3 rest on full text not read here. - go_id: GO:0032355 label: response to estradiol aspect: BP annotations: - UniProtKB:P06525 ADH1 (Arabidopsis, IEP) mechanism: IEP PMID:18441225 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP row(s) from UniProt on ADH1 rest on full text not read here. - go_id: GO:0006565 label: L-serine catabolic process aspect: BP annotations: - UniProtKB:D8RYU7 (Selaginella, IEA) - UniProtKB:D8SV17 (Selaginella, IEA) - UniProtKB:Q9MA74 SDC (Arabidopsis, IDA/IEA) mechanism: IEA ARBA:ARBA00097959; IDA PMID:39287621 (UniProt) verdict: FLAG_FAILS reason: Serine decarboxylase (SDC) consumes L-serine to make ethanolamine; IDA and ARBA rows are consistent. - go_id: GO:0003941 label: L-serine ammonia-lyase activity aspect: MF annotations: - UniProtKB:D8R3T5 (Selaginella, IBA/IEA) - UniProtKB:D8SIH3 (Selaginella, IBA/IEA) - UniProtKB:Q2PGG3 SR (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN000034721; IEA ARBA:ARBA00088741; IDA PMID:16483618 (UniProt); IEA EC:4.3.1.17; IEA RHEA:19169 verdict: FLAG_FAILS reason: Arabidopsis serine racemase has L-serine dehydratase activity (UniProt, IDA); IBA PTN000034721 is seeded by it and covers Selaginella orthologs. - go_id: GO:0004794 label: threonine deaminase activity aspect: MF annotations: - UniProtKB:D8QMP7 (Selaginella, IBA/IEA) - UniProtKB:D8R7H6 (Selaginella, IBA/IEA) - UniProtKB:Q9ZSS6 OMR1 (Arabidopsis, IBA/IDA/IEA/IMP) mechanism: IBA PANTHER:PTN002459384; IEA InterPro:IPR005787; IEA EC:4.3.1.19; IEA UniRule:UR000129796; IEA RHEA:22108; IEA ARBA:ARBA00026250; IDA PMID:28522547 (TAIR); IMP PMID:12228340 (TAIR) verdict: FLAG_FAILS reason: OMR1 threonine deaminase (isoleucine biosynthesis) is real in plants; IBA, InterPro, EC, RHEA and UniRule rows all agree. - go_id: GO:0042391 label: regulation of membrane potential aspect: BP annotations: - UniProtKB:Q38898 AKT2 (Arabidopsis, IMP) mechanism: IMP PMID:12172027 (TAIR) verdict: DEFER_TO_CURATOR reason: AKT2 is a K+ channel that sets phloem membrane potential; IMP is plausible, full text not read. - go_id: GO:0042391 label: regulation of membrane potential aspect: BP annotations: - UniProtKB:D8QXY5 (Selaginella, IBA) - UniProtKB:D8RUP6 (Selaginella, IBA) mechanism: IBA PANTHER:PTN000323131 verdict: UNCERTAIN reason: PTN000323131 is seeded by mouse Piezo1/Piezo2 and propagates to Selaginella PIEZO homologs. D8QXY5 is a PIEZO-telombin (POT1) fusion model. Plant PIEZO is largely tonoplast-localised, so "regulation of membrane potential" (a plasma-membrane depolarisation role in the seeds) is unproven. Settled by electrophysiology of a plant PIEZO. - go_id: GO:0001778 label: plasma membrane repair aspect: BP annotations: - UniProtKB:Q9SKR2 SYT1 (Arabidopsis, IMP) mechanism: IMP PMID:19088329 (TAIR) verdict: CONSTRAINT_QUESTIONABLE reason: The row breaks only_in_taxon Metazoa. Arabidopsis SYT1 is the established plant plasma-membrane integrity and resealing factor, so the constraint looks too narrow, not the IMP. - go_id: GO:0000372 label: Group I intron splicing aspect: BP annotations: - UniProtKB:Q8L7C2 CFM2 (Arabidopsis, IMP) mechanism: IMP PMID:18065687 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CFM2 rest on full text not read here. - go_id: GO:0043224 label: nuclear SCF ubiquitin ligase complex aspect: CC annotations: - UniProtKB:Q9ZR12 GRH1 (Arabidopsis, IDA) mechanism: IDA PMID:15992545 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on GRH1 rest on full text not read here. - go_id: GO:0003908 label: methylated-DNA-[protein]-cysteine S-methyltransferase activity aspect: MF annotations: - UniProtKB:F4I209 At1g63240 (Arabidopsis, IDA) mechanism: IDA PMID:33615694 (TAIR) verdict: UNCERTAIN reason: F4I209 (At1g63240) has only an MBD13-like region (IPR038945) and no MGMT signature. The paper reports a methyl-DNA binding protein (RMB1) in the ROS1 complex, not alkyl-transfer chemistry, so this looks like methyl-DNA binding mis-entered as MGMT activity. Settle it by confirming At1g63240 is RMB1 and that the full text has no methyltransferase assay; if so, use GO:0010385. replacement: GO:0010385 double-stranded methylated DNA binding (if confirmed) supported_by: - reference_id: PMID:33615694 supporting_text: RMB1 binds to DNA that is methylated in any sequence context - go_id: GO:0042178 label: xenobiotic catabolic process aspect: BP annotations: - UniProtKB:Q9M156 UGT72B1 (Arabidopsis, IDA) mechanism: IDA PMID:12753587 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on UGT72B1 rest on full text not read here. - go_id: GO:0015220 label: choline transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q94AN2 CHER1 (Arabidopsis, IDA) mechanism: IDA PMID:25008948 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CHER1 rest on full text not read here. - go_id: GO:0090554 label: phosphatidylcholine floppase activity aspect: MF annotations: - UniProtKB:Q9LI83 ALA10 (Arabidopsis, IDA) mechanism: IDA PMID:26212235 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ALA10 rest on full text not read here. - go_id: GO:0071629 label: cytoplasm protein quality control by the ubiquitin-proteasome system aspect: BP annotations: - UniProtKB:Q0WUQ1 BAG1 (Arabidopsis, IMP) - UniProtKB:Q9LQX2 MPSR1 (Arabidopsis, IMP) mechanism: IMP PMID:27343446 (TAIR); IMP PMID:29087340 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/UniProt on BAG1, MPSR1 rest on full text not read here. - go_id: GO:1990578 label: perinuclear endoplasmic reticulum membrane aspect: CC annotations: - UniProtKB:Q8VXU6 DI19-4 (Arabidopsis, IDA) mechanism: IDA PMID:16786289 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on DI19-4 rest on full text not read here. - go_id: GO:0015194 label: L-serine transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q42400 AAP1 (Arabidopsis, IMP) mechanism: IMP PMID:25005136 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on AAP1 rest on full text not read here. - go_id: GO:0006673 label: inositol phosphoceramide metabolic process aspect: BP annotations: - UniProtKB:Q8GWB7 IPUT1 (Arabidopsis, IDA) mechanism: IDA PMID:27643972 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on IPUT1 rest on full text not read here. - go_id: GO:0031398 label: positive regulation of protein ubiquitination aspect: BP annotations: - UniProtKB:F4K4R1 At5g49110 (Arabidopsis, IBA) - UniProtKB:Q9C901 At3g06610 (Arabidopsis, IMP) mechanism: IBA PANTHER:PTN000497925; IMP PMID:35524486 (TAIR) verdict: FLAG_FAILS reason: Q9C901 (HYPK homolog) IMP and the FANCI-like IBA (PTN000497925; FANCI promotes FANCD2 monoubiquitination) both fit conserved biology. - go_id: GO:0070328 label: triglyceride homeostasis aspect: BP annotations: - UniProtKB:O22975 At4g24160 (Arabidopsis, IMP) mechanism: IMP PMID:20876112 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At4g24160 rest on full text not read here. - go_id: GO:0019897 label: extrinsic component of plasma membrane aspect: CC annotations: - UniProtKB:Q8GYN5 RIN4 (Arabidopsis, IDA) mechanism: IDA PMID:22215637 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on RIN4 rest on full text not read here. - go_id: GO:0050201 label: fucokinase activity aspect: MF annotations: - UniProtKB:Q9LNJ9 FKGP (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN000794963; IDA PMID:18199744 (TAIR); IEA EC:2.7.1.52; IEA RHEA:13241 verdict: FLAG_FAILS reason: FKGP is the bifunctional plant fucokinase/GDP-fucose pyrophosphorylase; IDA, IBA and EC rows agree. - go_id: GO:0042352 label: GDP-L-fucose salvage aspect: BP annotations: - UniProtKB:Q9LNJ9 FKGP (Arabidopsis, IBA/IDA) mechanism: IBA PANTHER:PTN000794963; IDA PMID:18199744 (TAIR) verdict: FLAG_FAILS reason: FKGP salvages GDP-L-fucose in plants (IDA); the IBA is seeded by it. - go_id: GO:0015226 label: carnitine transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9CAT6 OCT1 (Arabidopsis, IDA) mechanism: IDA PMID:17521409 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on OCT1 rest on full text not read here. - go_id: GO:0035444 label: nickel cation transmembrane transport aspect: BP annotations: - UniProtKB:F4KGN5 IREG2 (Arabidopsis, IMP) mechanism: IMP PMID:16790430 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on IREG2 rest on full text not read here. - go_id: GO:0000041 label: transition metal ion transport aspect: BP annotations: - UniProtKB:F4KGN5 IREG2 (Arabidopsis, IMP) mechanism: IMP PMID:16790430 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on IREG2 rest on full text not read here. - go_id: GO:0052684 label: L-serine hydro-lyase (adding indole, L-tryptophan-forming) activity aspect: MF annotations: - UniProtKB:Q9FFW8 TSBTYPE2 (Arabidopsis, IDA) mechanism: IDA PMID:20701934 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on TSBTYPE2 rest on full text not read here. - go_id: GO:0044615 label: nuclear pore nuclear basket aspect: CC annotations: - UniProtKB:F4JPS3 At4g11790 (Arabidopsis, IDA) mechanism: IDA PMID:41206590 (TAIR) verdict: DEFER_TO_CURATOR reason: IDA nuclear basket localisation; plants have a basket (NUA/TPR, NUP1/136), full text not read. - go_id: GO:0044615 label: nuclear pore nuclear basket aspect: CC annotations: - UniProtKB:O04326 NUP35 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000488224 verdict: UNCERTAIN reason: PTN000488224 is seeded only by yeast NUP53, an inner-ring nucleoporin in most NPC models. Arabidopsis NUP35 inherits a basket location from that single seed. Settled by checking the SGD NUP53 basket evidence. - go_id: GO:0048041 label: focal adhesion assembly aspect: BP annotations: - UniProtKB:Q9LSR8 LECRK19 (Arabidopsis, IDA) mechanism: IDA PMID:16361528 (TAIR) verdict: ANNOTATION_WRONG reason: Focal adhesions are integrin-actin-ECM structures of animal cells. The paper shows LecRK-I.9 in plasma membrane-cell wall adhesions seen on plasmolysis, which is a different structure. GO defines cell-matrix adhesion as binding to the extracellular matrix, and the plant cell wall is not ECM in GO, so the candidate is the generic GO:0031589 cell-substrate adhesion; no GO term names plasma membrane-cell wall adhesion (ontology gap). replacement: GO:0031589 cell-substrate adhesion (candidate; ontology gap for membrane-wall adhesion) supported_by: - reference_id: PMID:16361528 supporting_text: Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis. - go_id: GO:0140677 label: molecular function activator activity aspect: MF annotations: - UniProtKB:O23661 ARF3 (Arabidopsis, IPI) mechanism: IPI PMID:30202032 (DisProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from DisProt on ARF3 rest on full text not read here. - go_id: GO:0009636 label: response to toxic substance aspect: BP annotations: - UniProtKB:Q9C5U2 AHK2 (Arabidopsis, IMP) - UniProtKB:Q9LUH2 DTX19 (Arabidopsis, ISS) - UniProtKB:Q9M156 UGT72B1 (Arabidopsis, IDA) mechanism: IMP PMID:17216481 (UniProt); ISS from PMID:11449055; IDA PMID:12753587 (TAIR) verdict: FLAG_FAILS reason: AHK2 IMP, UGT72B1 IDA (xenobiotic glucosylation) and the MATE transporter DTX19 ISS are all plausible for a broad stress term; rare only by curation density. - go_id: GO:0022604 label: regulation of cell morphogenesis aspect: BP annotations: - UniProtKB:F4I9A2 TNO1 (Arabidopsis, IMP) mechanism: IMP PMID:28399805 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on TNO1 rest on full text not read here. - go_id: GO:0035019 label: somatic stem cell population maintenance aspect: BP annotations: - UniProtKB:Q9XGW1 AGO10 (Arabidopsis, IMP) mechanism: IMP PMID:18653559 (UniProt) verdict: ANNOTATION_WRONG reason: The definition sets somatic stem cells against the germ line, a split shoot meristem stem cells do not obey because they later give rise to gametes. GO's descendants of this term are animal kidney terms. ZLL/AGO10 maintains shoot meristem stem cells, which the generic and meristem terms cover. replacement: GO:0019827 stem cell population maintenance (or GO:0010492 maintenance of shoot apical meristem identity) supported_by: - reference_id: PMID:18653559 supporting_text: ZLL acts to maintain the stem cells from the neighbouring vascular primordium - go_id: GO:0051721 label: protein phosphatase 2A binding aspect: MF annotations: - UniProtKB:Q941D6 HDA14 (Arabidopsis, IDA) mechanism: IDA PMID:22404109 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on HDA14 rest on full text not read here. - go_id: GO:0006688 label: glycosphingolipid biosynthetic process aspect: BP annotations: - UniProtKB:Q9LY62 GMT1 (Arabidopsis, IMP) mechanism: IMP PMID:27895225 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on GMT1 rest on full text not read here. - go_id: GO:1904408 label: melatonin binding aspect: MF annotations: - UniProtKB:Q94AH1 CAND2 (Arabidopsis, IDA) mechanism: IDA PMID:29702752 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CAND2 rest on full text not read here. - go_id: GO:0019740 label: nitrogen utilization aspect: BP annotations: - UniProtKB:Q43314 GDH1 (Arabidopsis, IMP) - UniProtKB:Q8L8Y3 CEP1 (Arabidopsis, IEP) mechanism: IMP PMID:8643469 (TAIR); IEP PMID:24179095 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP/IMP row(s) from TAIR/UniProt on CEP1, GDH1 rest on full text not read here. - go_id: GO:0030155 label: regulation of cell adhesion aspect: BP annotations: - UniProtKB:Q42371 ERECTA (Arabidopsis, IMP) mechanism: IMP PMID:16007076 (TAIR) verdict: DEFER_TO_CURATOR reason: ERECTA IMP; regulation of cell adhesion can apply to plant cells (wall-mediated adhesion), full text not read. - go_id: GO:0030155 label: regulation of cell adhesion aspect: BP annotations: - UniProtKB:Q9LFC0 HAKAI (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN000336748 verdict: ANNOTATION_WRONG reason: Plants have no cadherins, and plant HAKAI works as an m6A-writer subunit, so the adhesion function (Hakai ubiquitinates E-cadherin) arose in an animal lineage below PTN000336748 and the plant proteins are outside the clade that inherited it. - go_id: GO:0015755 label: fructose transmembrane transport aspect: BP annotations: - UniProtKB:Q84WN3 SWEET17 (Arabidopsis, IMP) - UniProtKB:Q8L6Z8 At3g03090 (Arabidopsis, IDA) mechanism: IMP PMID:24381066 (UniProt); IDA PMID:17284600 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on At3g03090, SWEET17 rest on full text not read here. - go_id: GO:0071281 label: cellular response to iron ion aspect: BP annotations: - UniProtKB:Q96262 PCAP1 (Arabidopsis, IEP) - UniProtKB:Q9SZ46 CYP82C4 (Arabidopsis, IEP) mechanism: IEP PMID:17264065 (UniProt); IEP PMID:21315474 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP row(s) from TAIR/UniProt on CYP82C4, PCAP1 rest on full text not read here. - go_id: GO:0050850 label: positive regulation of calcium-mediated signaling aspect: BP annotations: - UniProtKB:F4I5N6 RIC3 (Arabidopsis, IMP) mechanism: IMP PMID:15824136 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on RIC3 rest on full text not read here. - go_id: GO:0016682 label: oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor aspect: MF annotations: - UniProtKB:Q39224 SRG1 (Arabidopsis, ISS) mechanism: ISS from PMID:8883383 verdict: ANNOTATION_WRONG reason: SRG1 belongs to the Fe(II)/ascorbate-dependent (2OG) dioxygenase family. The 1996 ISS appears to have read "ascorbate oxidase superfamily" as the multicopper diphenol/ascorbate oxidases (EC 1.10.3.x), a different fold. replacement: GO:0016706 2-oxoglutarate-dependent dioxygenase activity (family level) supported_by: - reference_id: PMID:8883383 supporting_text: Amino acid sequence analysis shows that the putative SRG1 protein is a new member of the Fe(II)/ascorbate oxidase superfamily - go_id: GO:0016682 label: oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor aspect: MF annotations: - UniProtKB:F4I4K5 LPR1 (Arabidopsis, IDA) mechanism: IDA PMID:17496893 (TAIR) verdict: DEFER_TO_CURATOR reason: LPR1 is a multicopper oxidase (ferroxidase); the term can apply, and the IDA rests on full text not read. - go_id: GO:0016682 label: oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor aspect: MF annotations: - UniProtKB:C7B2F5 psbA (Selaginella, IEA) mechanism: IEA UniRule:UR000352928 verdict: FLAG_FAILS reason: The UniRule maps PSII D1 (EC 1.10.3.9, plastoquinone/water oxidoreductase) to this term, which follows the EC hierarchy (EC 1.10.3). It is formally consistent; the rarity is because other plant psbA records lack this rule. - go_id: GO:0010647 label: positive regulation of cell communication aspect: BP annotations: - UniProtKB:Q9SEU7 GAT1 (Arabidopsis, IMP) mechanism: IMP PMID:19218459 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on GAT1 rest on full text not read here. - go_id: GO:0008053 label: mitochondrial fusion aspect: BP annotations: - UniProtKB:Q9C542 At1g55160 (Arabidopsis, IMP) - UniProtKB:Q9ZUN9 At2g19530 (Arabidopsis, IMP) mechanism: IMP PMID:42018423 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on At1g55160, At2g19530 rest on full text not read here. - go_id: GO:0090292 label: nuclear matrix anchoring at nuclear membrane aspect: BP annotations: - UniProtKB:F4KG14 GBPL3 (Arabidopsis, IDA/IPI) mechanism: IDA PMID:36269771 (TAIR); IPI PMID:36269771 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IPI row(s) from TAIR on GBPL3 rest on full text not read here. - go_id: GO:0023056 label: positive regulation of signaling aspect: BP annotations: - UniProtKB:Q9SD42 RTH (Arabidopsis, IGI) mechanism: IGI PMID:28541511 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on RTH rest on full text not read here. - go_id: GO:0032206 label: positive regulation of telomere maintenance aspect: BP annotations: - UniProtKB:Q56Y52 POT1A (Arabidopsis, IMP) mechanism: IMP PMID:16107718 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on POT1A rest on full text not read here. - go_id: GO:0034775 label: glutathione transmembrane transport aspect: BP annotations: - UniProtKB:Q680I5 GGT2 (Arabidopsis, IMP) mechanism: IMP PMID:20959624 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on GGT2 rest on full text not read here. - go_id: GO:1901612 label: cardiolipin binding aspect: MF annotations: - UniProtKB:Q9ASV5 MIC60 (Arabidopsis, IDA) mechanism: IDA PMID:26898467 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on MIC60 rest on full text not read here. - go_id: GO:0035024 label: negative regulation of Rho protein signal transduction aspect: BP annotations: - UniProtKB:F4JQZ3 REN1 (Arabidopsis, IMP) mechanism: IMP PMID:19108776 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on REN1 rest on full text not read here. - go_id: GO:0140008 label: histone H4 reader activity aspect: MF annotations: - UniProtKB:F4IAE9 At1g05910 (Arabidopsis, IDA) mechanism: IDA PMID:27273316 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on At1g05910 rest on full text not read here. - go_id: GO:0046827 label: positive regulation of protein export from nucleus aspect: BP annotations: - UniProtKB:Q39011 ASK7 (Arabidopsis, IDA) mechanism: IDA PMID:17873094 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ASK7 rest on full text not read here. - go_id: GO:0010828 label: positive regulation of D-glucose transmembrane transport aspect: BP annotations: - UniProtKB:Q9XI87 VIK (Arabidopsis, IMP) mechanism: IMP PMID:21838775 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on VIK rest on full text not read here. - go_id: GO:0000292 label: RNA fragment catabolic process aspect: BP annotations: - UniProtKB:F4JAA5 SKI2 (Arabidopsis, IMP) mechanism: IMP PMID:26464441 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on SKI2 rest on full text not read here. - go_id: GO:0006793 label: phosphorus metabolic process aspect: BP annotations: - UniProtKB:Q93Z81 CAX3 (Arabidopsis, IGI) mechanism: IGI PMID:16055687 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on CAX3 rest on full text not read here. - go_id: GO:0031941 label: filamentous actin aspect: CC annotations: - UniProtKB:Q94KK5 SYP73 (Arabidopsis, IDA) mechanism: IDA PMID:27866894 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SYP73 rest on full text not read here. - go_id: GO:0051247 label: positive regulation of protein metabolic process aspect: BP annotations: - UniProtKB:Q3E7K4 QQS (Arabidopsis, IMP) - UniProtKB:Q9FMV5 NFYC4 (Arabidopsis, IMP) mechanism: IMP PMID:26554020 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on NFYC4, QQS rest on full text not read here. - go_id: GO:0030971 label: receptor tyrosine kinase binding aspect: MF annotations: - UniProtKB:P94040 GLP1 (Arabidopsis, IPI) - UniProtKB:P94072 GER3 (Arabidopsis, IPI) mechanism: IPI PMID:37979582 (TAIR) verdict: ANNOTATION_WRONG reason: The partner in with_from, TMK1 (AT1G66150), is a serine/threonine receptor kinase (UniProt EC 2.7.11.1 only), and the paper does not mention tyrosine. Germin-like ABL1/ABL2 binding to the TMK1 ectodomain needs the Ser/Thr receptor term. replacement: GO:0070696 transmembrane receptor protein serine/threonine kinase binding - go_id: GO:0032008 label: positive regulation of TOR signaling aspect: BP annotations: - UniProtKB:Q8LDQ4 TAP46 (Arabidopsis, IMP) - UniProtKB:Q9SLA6 ISE3 (Arabidopsis, IBA) mechanism: IMP PMID:25399018 (UniProt); IBA PANTHER:PTN008690749 verdict: FLAG_FAILS reason: TAP46 IMP and the At2g25570 IBA (PTN008690749, seeded by its Brassica rapa ortholog with IMP) both describe plant TOR-pathway factors. - go_id: GO:2000036 label: regulation of stem cell population maintenance aspect: BP annotations: - UniProtKB:Q9LKZ3 RBR1 (Arabidopsis, IMP) mechanism: IMP PMID:16377572 (TAIR); IMP PMID:20525851 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/UniProt on RBR1 rest on full text not read here. - go_id: GO:0097009 label: energy homeostasis aspect: BP annotations: - UniProtKB:Q7X9B9 NLP2 (Arabidopsis, IMP) - UniProtKB:Q9FIJ7 At5g47840 (Arabidopsis, IMP) mechanism: IMP PMID:36752317 (TAIR); IMP PMID:18162585 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/UniProt on At5g47840, NLP2 rest on full text not read here. - go_id: GO:0004382 label: GDP phosphatase activity aspect: MF annotations: - UniProtKB:Q9SQG2 APY1 (Arabidopsis, IDA) mechanism: IDA PMID:22849572 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on APY1 rest on full text not read here. - go_id: GO:0004321 label: fatty-acyl-CoA synthase activity aspect: MF annotations: - UniProtKB:Q84P23 4CLL9 (Arabidopsis, IDA) - UniProtKB:Q9M0X9 4CLL7 (Arabidopsis, IDA) mechanism: IDA PMID:15677481 (TAIR) verdict: ANNOTATION_WRONG reason: 'Synthase/synthetase confusion: GO:0004321 is fatty acid synthase chemistry (acetyl-CoA + malonyl-CoA + NAD(P)H). 4CLL7 and 4CLL9 are ATP-dependent acyl-CoA ligases (EC 6.2.1.-) that activate free medium- and long-chain fatty acids and OPDA.' replacement: GO:0004467 long-chain fatty acid-CoA ligase activity; GO:0031956 medium-chain fatty acid-CoA ligase activity supported_by: - reference_id: PMID:15677481 supporting_text: This study uncovered a significant activity of At4g05160 with medium-chain fatty acids - go_id: GO:0015927 label: trehalase activity aspect: MF annotations: - UniProtKB:Q9SU50 TRE1 (Arabidopsis, IEA) mechanism: IEA ARBA:ARBA00026767 verdict: FLAG_FAILS reason: TRE1 is the Arabidopsis trehalase (UniProt function), so the ARBA IEA is right. - go_id: GO:0015927 label: trehalase activity aspect: MF annotations: - UniProtKB:Q67XC9 TPPD (Arabidopsis, IDA) mechanism: IDA PMID:24800789 (TAIR) verdict: UNCERTAIN reason: Q67XC9 is TPPD, a trehalose-6-phosphate phosphatase, and the paper's abstract describes only TPP activity and its redox control. Trehalase activity is probably a mis-selected term; settle by checking the full text for any trehalose-hydrolysis assay. replacement: GO:0004805 trehalose-phosphatase activity (if no trehalase assay) - go_id: GO:0002218 label: activation of innate immune response aspect: BP annotations: - UniProtKB:F4HT77 RBA1 (Arabidopsis, IDA) - UniProtKB:F4J2I0 ACIP1 (Arabidopsis, IMP) mechanism: IDA PMID:35597242 (UniProt); IMP PMID:24586161 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on ACIP1, RBA1 rest on full text not read here. - go_id: GO:0045134 label: UDP phosphatase activity aspect: MF annotations: - UniProtKB:Q9SQG2 APY1 (Arabidopsis, IDA) mechanism: IDA PMID:22849572 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on APY1 rest on full text not read here. - go_id: GO:0071453 label: cellular response to oxygen levels aspect: BP annotations: - UniProtKB:Q9C8N5 STOP1 (Arabidopsis, IMP) mechanism: IMP PMID:30882866 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on STOP1 rest on full text not read here. - go_id: GO:0015129 label: lactate transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q8W037 NIP2-1 (Arabidopsis, IDA) mechanism: IDA PMID:17584741 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on NIP2-1 rest on full text not read here. - go_id: GO:0052816 label: long-chain fatty acyl-CoA hydrolase activity aspect: MF annotations: - UniProtKB:F4HU51 ACH2 (Arabidopsis, IDA) - UniProtKB:Q5FYU1 CNTE1 (Arabidopsis, ISS) mechanism: IDA PMID:14660652 (UniProt); ISS from UniProtKB:F4HU51 verdict: FLAG_FAILS reason: Acyl-CoA thioesterase IDA on F4HU51 and an ISS to its paralog Q5FYU1; correct, rare only by curation density. - go_id: GO:0004040 label: amidase activity aspect: MF annotations: - UniProtKB:A0A1P8B760 At4g34880 (Arabidopsis, IEA/ISS) - UniProtKB:Q9FR37 AMI1 (Arabidopsis, EXP/IDA/IEA) mechanism: IEA EC:3.5.1.4; IEA RHEA:12020; ISS from UniProtKB:Q9FR37; EXP PMID:12620340 (UniProt); EXP PMID:27135507 (UniProt); IDA PMID:17555521 (TAIR); IEA RHEA:64820 verdict: FLAG_FAILS reason: AMI1 is a characterised amidase (EXP/IDA). The EC/RHEA IEA rows and the ISS to At4g34880 follow from the amidase signature family. - go_id: GO:0019154 label: glycolate dehydrogenase activity aspect: MF annotations: - UniProtKB:Q94AX4 DLD (Arabidopsis, IDA) mechanism: IDA PMID:14966218 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on DLD rest on full text not read here. - go_id: GO:0019213 label: deacetylase activity aspect: MF annotations: - UniProtKB:D8RLU6 (Selaginella, IBA) - UniProtKB:Q941D6 HDA14 (Arabidopsis, IDA) - UniProtKB:Q94AQ6 SRT2 (Arabidopsis, IDA) mechanism: IBA PANTHER:PTN000833391; IDA PMID:29247559 (UniProt); IDA PMID:24424322 (TAIR) verdict: FLAG_FAILS reason: HDA14 (protein lysine deacetylase) and Q94AQ6 IDA plus a NodB polysaccharide-deacetylase IBA seeded by chitin deacetylases; all are deacetylases, and the term is general but true. - go_id: GO:0050714 label: positive regulation of protein secretion aspect: BP annotations: - UniProtKB:F4K183 At5g26740 (Arabidopsis, IGI) - UniProtKB:Q9SFF8 At3g05940 (Arabidopsis, IGI) mechanism: IGI PMID:39405432 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on At3g05940, At5g26740 rest on full text not read here. - go_id: GO:0043457 label: regulation of cellular respiration aspect: BP annotations: - UniProtKB:Q41188 CSP2 (Arabidopsis, IMP) mechanism: IMP PMID:17376161 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on CSP2 rest on full text not read here. - go_id: GO:1905323 label: telomerase holoenzyme complex assembly aspect: BP annotations: - UniProtKB:Q9FMR9 RIN1 (Arabidopsis, IMP) mechanism: IMP PMID:30834599 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on RIN1 rest on full text not read here. - go_id: GO:0090148 label: membrane fission aspect: BP annotations: - UniProtKB:Q9LVF4 DMP1 (Arabidopsis, IDA) mechanism: IDA PMID:22530652 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on DMP1 rest on full text not read here. - go_id: GO:0098562 label: cytoplasmic side of membrane aspect: CC annotations: - UniProtKB:Q6F6B5 ARC3 (Arabidopsis, IDA) mechanism: IDA PMID:15356321 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on ARC3 rest on full text not read here. - go_id: GO:1990814 label: DNA/DNA annealing activity aspect: MF annotations: - UniProtKB:Q9FT72 RECQL3 (Arabidopsis, IDA) mechanism: IDA PMID:19755539 (GO_Central) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from GO_Central on RECQL3 rest on full text not read here. - go_id: GO:0034089 label: establishment of meiotic sister chromatid cohesion aspect: BP annotations: - UniProtKB:A7UL74 CTF7 (Arabidopsis, IMP) mechanism: IMP PMID:23750584 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CTF7 rest on full text not read here. - go_id: GO:0015183 label: L-aspartate transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9SS86 At3g01760 (Arabidopsis, IMP) mechanism: IMP PMID:25005136 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At3g01760 rest on full text not read here. - go_id: GO:0070778 label: L-aspartate transmembrane transport aspect: BP annotations: - UniProtKB:Q9SS86 At3g01760 (Arabidopsis, IMP) mechanism: IMP PMID:25005136 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At3g01760 rest on full text not read here. - go_id: GO:0000262 label: mitochondrial chromosome aspect: CC annotations: - UniProtKB:Q9C504 SWIB5 (Arabidopsis, IDA) - UniProtKB:Q9M219 MTERF18 (Arabidopsis, IDA) mechanism: IDA PMID:28420746 (TAIR); IDA PMID:34482561 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on MTERF18, SWIB5 rest on full text not read here. - go_id: GO:0090306 label: meiotic spindle assembly aspect: BP annotations: - UniProtKB:A9QM73 SMG7 (Arabidopsis, IMP) mechanism: IMP PMID:18544632 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on SMG7 rest on full text not read here. - go_id: GO:0046354 label: mannan biosynthetic process aspect: BP annotations: - UniProtKB:Q0WPA5 MSR2 (Arabidopsis, IMP) - UniProtKB:Q9LU40 MSR1 (Arabidopsis, IMP) mechanism: IMP PMID:22966747 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on MSR1, MSR2 rest on full text not read here. - go_id: GO:0032212 label: positive regulation of telomere maintenance via telomerase aspect: BP annotations: - UniProtKB:Q56Y52 POT1A (Arabidopsis, IMP) mechanism: IMP PMID:17627276 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on POT1A rest on full text not read here. - go_id: GO:0000900 label: mRNA regulatory element binding translation repressor activity aspect: MF annotations: - UniProtKB:Q9FVC1 SVP (Arabidopsis, IDA) mechanism: IDA PMID:17322399 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SVP rest on full text not read here. - go_id: GO:1903077 label: negative regulation of protein localization to plasma membrane aspect: BP annotations: - UniProtKB:O64425 RMA1 (Arabidopsis, IMP) mechanism: IMP PMID:19234086 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on RMA1 rest on full text not read here. - go_id: GO:0045143 label: homologous chromosome segregation aspect: BP annotations: - UniProtKB:F4JEP5 MSH5 (Arabidopsis, IMP) - UniProtKB:F4JP48 MSH4 (Arabidopsis, IMP) mechanism: IMP PMID:18318687 (UniProt); IMP PMID:15489296 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on MSH4, MSH5 rest on full text not read here. - go_id: GO:0010314 label: phosphatidylinositol-5-phosphate binding aspect: MF annotations: - UniProtKB:Q9C5X4 ATX1 (Arabidopsis, IDA) - UniProtKB:Q9FG74 D6PK (Arabidopsis, IDA) mechanism: IDA PMID:16585509 (TAIR); IDA PMID:27251533 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR/UniProt on ATX1, D6PK rest on full text not read here. - go_id: GO:0009303 label: rRNA transcription aspect: BP annotations: - UniProtKB:Q8H1E7 NOF1 (Arabidopsis, IMP) - UniProtKB:Q9FR53 TOR (Arabidopsis, IMP) mechanism: IMP PMID:20877469 (TAIR); IMP PMID:21266656 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on NOF1, TOR rest on full text not read here. - go_id: GO:0015431 label: ABC-type glutathione S-conjugate transporter activity aspect: MF annotations: - UniProtKB:Q9LK64 ABCC3 (Arabidopsis, IDA) mechanism: IDA PMID:9681016 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ABCC3 rest on full text not read here. - go_id: GO:0031054 label: pre-miRNA processing aspect: BP annotations: - UniProtKB:O04492 DRB1 (Arabidopsis, IMP) mechanism: IMP PMID:16428603 (UniProt); IMP PMID:17337628 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on DRB1 rest on full text not read here. - go_id: GO:0045786 label: negative regulation of cell cycle aspect: BP annotations: - UniProtKB:Q8GYJ3 KRP4 (Arabidopsis, TAS) - UniProtKB:Q9LZ78 SIM (Arabidopsis, IMP) mechanism: TAS PMID:15037450 (TAIR); IMP PMID:26561564 (TAIR) verdict: FLAG_FAILS reason: Plant cell-cycle inhibitors (IMP, TAS); the term is generic and applies to plants. - go_id: GO:0031396 label: regulation of protein ubiquitination aspect: BP annotations: - UniProtKB:O22286 BPM3 (Arabidopsis, IMP) mechanism: IMP PMID:22172674 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on BPM3 rest on full text not read here. - go_id: GO:0009268 label: response to pH aspect: BP annotations: - UniProtKB:O22932 CIPK11 (Arabidopsis, IMP) mechanism: IMP PMID:17483306 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CIPK11 rest on full text not read here. - go_id: GO:0089718 label: amino acid import across plasma membrane aspect: BP annotations: - UniProtKB:Q84MA5 CAT1 (Arabidopsis, IDA/IMP) mechanism: IDA PMID:8618839 (UniProt); IMP PMID:24895758 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from UniProt on CAT1 rest on full text not read here. - go_id: GO:0110154 label: RNA decapping aspect: BP annotations: - UniProtKB:Q8RY73 DXO1 (Arabidopsis, IDA) mechanism: IDA PMID:31449356 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on DXO1 rest on full text not read here. - go_id: GO:1990169 label: stress response to copper ion aspect: BP annotations: - UniProtKB:Q9FJ47 SAG12 (Arabidopsis, IEP) mechanism: IEP PMID:10380810 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP row(s) from UniProt on SAG12 rest on full text not read here. - go_id: GO:0090316 label: positive regulation of intracellular protein transport aspect: BP annotations: - UniProtKB:Q5PNU3 AMSH3 (Arabidopsis, IMP) mechanism: IMP PMID:20543027 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on AMSH3 rest on full text not read here. - go_id: GO:0015810 label: aspartate transmembrane transport aspect: BP annotations: - UniProtKB:P92934 AAP6 (Arabidopsis, IDA) mechanism: IDA PMID:12148530 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on AAP6 rest on full text not read here. - go_id: GO:0008126 label: acetylesterase activity aspect: MF annotations: - UniProtKB:Q9STM6 At3g48460 (Arabidopsis, IDA) mechanism: IDA PMID:28510842 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on At3g48460 rest on full text not read here. - go_id: GO:0042770 label: signal transduction in response to DNA damage aspect: BP annotations: - UniProtKB:Q9FV70 E2FC (Arabidopsis, IMP) mechanism: IMP PMID:30427087 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on E2FC rest on full text not read here. - go_id: GO:0005641 label: nuclear envelope lumen aspect: CC annotations: - UniProtKB:F4J1U4 KIN12E (Arabidopsis, IDA) mechanism: IDA PMID:33751090 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on KIN12E rest on full text not read here. - go_id: GO:0047681 label: aryl-alcohol dehydrogenase (NADP+) activity aspect: MF annotations: - UniProtKB:Q02972 CAD8 (Arabidopsis, IDA) mechanism: IDA PMID:11038530 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CAD8 rest on full text not read here. - go_id: GO:0033120 label: positive regulation of RNA splicing aspect: BP annotations: - UniProtKB:F4K2E9 CUV (Arabidopsis, IMP) mechanism: IMP PMID:25384462 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on CUV rest on full text not read here. - go_id: GO:0120542 label: ethanol dehydrogenase (NAD+) activity aspect: MF annotations: - UniProtKB:P06525 ADH1 (Arabidopsis, EXP/IEA) mechanism: EXP PMID:38308388 (UniProt); IEA RHEA:25290 verdict: FLAG_FAILS reason: ADH1 ethanol dehydrogenase (EXP) with a matching RHEA IEA; correct. - go_id: GO:0061692 label: cellular detoxification of hydrogen peroxide aspect: BP annotations: - UniProtKB:Q9T0H4 ADR (Arabidopsis, IMP) mechanism: IMP PMID:30911018 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on ADR rest on full text not read here. - go_id: GO:0006642 label: triglyceride mobilization aspect: BP annotations: - UniProtKB:Q9SKP6 TIM (Arabidopsis, IMP) mechanism: IMP PMID:20097871 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on TIM rest on full text not read here. - go_id: GO:0043633 label: polyadenylation-dependent RNA catabolic process aspect: BP annotations: - UniProtKB:A9LLI7 RRP6L2 (Arabidopsis, IMP) mechanism: IMP PMID:18285452 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on RRP6L2 rest on full text not read here. - go_id: GO:0042762 label: regulation of sulfur metabolic process aspect: BP annotations: - UniProtKB:O23116 EIL3 (Arabidopsis, IMP) mechanism: IMP PMID:17114350 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on EIL3 rest on full text not read here. - go_id: GO:0034214 label: protein hexamerization aspect: BP annotations: - UniProtKB:P46637 ARGAH1 (Arabidopsis, IDA) - UniProtKB:Q9LQF2 CINV1 (Arabidopsis, IDA) mechanism: IDA PMID:32754173 (UniProt); IDA PMID:32134001 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on ARGAH1, CINV1 rest on full text not read here. - go_id: GO:1990238 label: double-stranded DNA endonuclease activity aspect: MF annotations: - UniProtKB:Q9C9G4 ENDO2 (Arabidopsis, IDA) - UniProtKB:Q9SXA6 ENDO1 (Arabidopsis, IDA) mechanism: IDA PMID:23620482 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on ENDO1, ENDO2 rest on full text not read here. - go_id: GO:0033212 label: iron import into cell aspect: BP annotations: - UniProtKB:F4HVS0 At1g74770 (Arabidopsis, IMP) - UniProtKB:F4IDY5 At1g18910 (Arabidopsis, IMP) mechanism: IMP PMID:31413196 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At1g18910, At1g74770 rest on full text not read here. - go_id: GO:0033011 label: perinuclear theca aspect: CC annotations: - UniProtKB:Q8L706 SYT5 (Arabidopsis, IDA) mechanism: IDA PMID:34504049 (TAIR) verdict: ANNOTATION_WRONG reason: Perinuclear theca is by definition a structure of mammalian spermatozoa. The paper found SYT5 in the perinuclear area of root cells, mostly in the ER. replacement: GO:0048471 perinuclear region of cytoplasm (and GO:0005783 endoplasmic reticulum) supported_by: - reference_id: PMID:34504049 supporting_text: we detected immuno-fluorescently marked SYT5 in perinuclear area - reference_id: PMID:34504049 supporting_text: indicate that SYT5 is largely localized to the ER - go_id: GO:0019395 label: fatty acid oxidation aspect: BP annotations: - UniProtKB:Q9LZ31 CYP77A4 (Arabidopsis, IDA) mechanism: IDA PMID:19120447 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CYP77A4 rest on full text not read here. - go_id: GO:2000042 label: negative regulation of double-strand break repair via homologous recombination aspect: BP annotations: - UniProtKB:A0A1P8AN39 RMI2 (Arabidopsis, IMP) - UniProtKB:F4HW22 RMI2 (Arabidopsis, IMP) mechanism: IMP PMID:27760121 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on RMI2 rest on full text not read here. - go_id: GO:0045930 label: negative regulation of mitotic cell cycle aspect: BP annotations: - UniProtKB:Q9SZF7 SHR (Arabidopsis, IBA/IMP) mechanism: IBA PANTHER:PTN001587390; IMP PMID:20739610 (TAIR) verdict: FLAG_FAILS reason: IBA PTN001587390 seeded by Q9SZF7 itself plus its IMP; consistent. - go_id: GO:0004064 label: arylesterase activity aspect: MF annotations: - UniProtKB:Q9SYF0 GLIP2 (Arabidopsis, IDA) mechanism: IDA PMID:19146828 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on GLIP2 rest on full text not read here. - go_id: GO:0030332 label: cyclin binding aspect: MF annotations: - UniProtKB:Q2V419 CDKB1-2 (Arabidopsis, IPI) mechanism: IPI PMID:11432958 (TAIR) verdict: ANNOTATION_WRONG reason: The IPI partner in with_from is AT2G27960, which is CKS1, a CDK-docking subunit and not a cyclin. The paper is a CKS1 two-hybrid screen that pulled out CDKB1;2. This row records CKS1 binding, not cyclin binding. supported_by: - reference_id: PMID:11432958 supporting_text: With the Arabidopsis thaliana CKS1At protein as bait in a two-hybrid screen, two novel Arabidopsis CDKs, Arath;CDKB1;2 and Arath;CDKB2;1, were isolated. - go_id: GO:0030332 label: cyclin binding aspect: MF annotations: - UniProtKB:Q9LW36 At3g26750 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN001585923 verdict: UNCERTAIN reason: PTN001585923 is seeded only by human UBE3D (UbcH10-binding protein), whose cyclin B1 link is animal-specific. The Arabidopsis homolog At3g26750 has no reported partners. Settled by an interaction test. - go_id: GO:0051924 label: regulation of calcium ion transport aspect: BP annotations: - UniProtKB:F4HX37 At1g62045 (Arabidopsis, IGI) - UniProtKB:Q9FLJ8 At5g61350 (Arabidopsis, IMP) mechanism: IGI PMID:37995686 (TAIR); IMP PMID:24769480 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IMP row(s) from TAIR on At1g62045, At5g61350 rest on full text not read here. - go_id: GO:0006720 label: isoprenoid metabolic process aspect: BP annotations: - UniProtKB:Q67ZM7 FOLK (Arabidopsis, IDA) mechanism: IDA PMID:21395888 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on FOLK rest on full text not read here. - go_id: GO:0042167 label: heme catabolic process aspect: BP annotations: - UniProtKB:Q8LDU1 HOZ (Arabidopsis, IDA) mechanism: IDA PMID:33284325 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on HOZ rest on full text not read here. - go_id: GO:0006218 label: uridine catabolic process aspect: BP annotations: - UniProtKB:Q9SJM7 URH1 (Arabidopsis, IBA/IMP) mechanism: IBA PANTHER:PTN000266727; IMP PMID:19293370 (TAIR) verdict: FLAG_FAILS reason: NSH1 uridine nucleosidase drives uridine catabolism (IMP); IBA seeded by NSH1 and yeast URH1. - go_id: GO:1903424 label: fluoride transmembrane transport aspect: BP annotations: - UniProtKB:Q8RYE2 FEX (Arabidopsis, IGI) mechanism: IGI PMID:28472134 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on FEX rest on full text not read here. - go_id: GO:0015882 label: L-ascorbic acid transmembrane transport aspect: BP annotations: - UniProtKB:Q8GX78 PHT4;4 (Arabidopsis, IDA) mechanism: IDA PMID:25557369 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PHT4;4 rest on full text not read here. - go_id: GO:0015415 label: ATPase-coupled phosphate ion transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9S735 PHT1-9 (Arabidopsis, IDA) mechanism: IDA PMID:22578268 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PHT1-9 rest on full text not read here. - go_id: GO:0005353 label: fructose transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q84WN3 SWEET17 (Arabidopsis, IMP) - UniProtKB:Q8L6Z8 At3g03090 (Arabidopsis, IDA) - UniProtKB:Q9LUR4 SWEET16 (Arabidopsis, IDA) mechanism: IMP PMID:23583552 (UniProt); IDA PMID:17284600 (TAIR); IDA PMID:24028846 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on At3g03090, SWEET16, SWEET17 rest on full text not read here. - go_id: GO:0031435 label: mitogen-activated protein kinase kinase kinase binding aspect: MF annotations: - UniProtKB:Q9FJV0 MKK6 (Arabidopsis, IPI) mechanism: IPI PMID:30185442 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on MKK6 rest on full text not read here. - go_id: GO:0001935 label: endothelial cell proliferation aspect: BP annotations: - UniProtKB:Q6R053 MYB56 (Arabidopsis, IMP) mechanism: IMP PMID:23911125 (UniProt) verdict: ANNOTATION_WRONG reason: GO's endothelial cells line animal blood and lymph vessels. MYB56 acts on the seed-coat "endothelium" (inner integument layer), a homonym, and the cell-number change is in the outer integument. replacement: GO:0010214 seed coat development supported_by: - reference_id: PMID:23911125 supporting_text: myb56 developed smaller contracted endothelial cells and reduced cell number in the outer integument layer of the seed coat - go_id: GO:0052629 label: phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity aspect: MF annotations: - UniProtKB:F4J3T8 MTM1 (Arabidopsis, IDA/IEA) - UniProtKB:F4JWB3 MTM2 (Arabidopsis, IDA/IEA) mechanism: IDA PMID:19901554 (TAIR); IDA PMID:22324391 (UniProt); IEA EC:3.1.3.95; IEA RHEA:39019 verdict: FLAG_FAILS reason: Arabidopsis myotubularins (AtMTM1/2) dephosphorylate PI(3,5)P2 (IDA); EC/RHEA IEA rows follow. - go_id: GO:0032006 label: regulation of TOR signaling aspect: BP annotations: - UniProtKB:F4JFA0 THADA (Arabidopsis, IMP) mechanism: IMP PMID:30098100 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on THADA rest on full text not read here. - go_id: GO:0051050 label: positive regulation of transport aspect: BP annotations: - UniProtKB:Q94K05 CCT8 (Arabidopsis, IMP) mechanism: IMP PMID:21868675 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on CCT8 rest on full text not read here. - go_id: GO:0045089 label: positive regulation of innate immune response aspect: BP annotations: - UniProtKB:Q9SCP5 UGT73C7 (Arabidopsis, IGI) - UniProtKB:Q9SKB2 SOBIR1 (Arabidopsis, EXP) mechanism: IGI PMID:33866633 (TAIR); EXP PMID:24259685 (PHI-base) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; EXP/IGI row(s) from PHI-base/TAIR on SOBIR1, UGT73C7 rest on full text not read here. - go_id: GO:0009967 label: positive regulation of signal transduction aspect: BP annotations: - UniProtKB:O24456 RACK1A (Arabidopsis, IEA/IMP) - UniProtKB:Q9C4Z6 RACK1B (Arabidopsis, IEA/IMP) - UniProtKB:Q9LV28 RACK1C (Arabidopsis, IEA/IMP) mechanism: IEA ARBA:ARBA00027202; IMP PMID:25731164 (UniProt) verdict: FLAG_FAILS reason: RACK1A/B/C IMP and ARBA IEA agree on a generic signalling term that applies to plants. - go_id: GO:0008509 label: monoatomic anion transmembrane transporter activity aspect: MF annotations: - UniProtKB:O49696 ALMT12 (Arabidopsis, IDA) - UniProtKB:Q9LD83 SLAC1 (Arabidopsis, IDA) mechanism: IDA PMID:20154005 (TAIR); IDA DOI:10.1038/nature09487 (UniProt); IDA PMID:18305484 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR/UniProt on ALMT12, SLAC1 rest on full text not read here. - go_id: GO:0006307 label: DNA alkylation repair aspect: BP annotations: - UniProtKB:F4HXH4 At1g75230 (Arabidopsis, IBA) - UniProtKB:Q9SIE0 ALKBH2 (Arabidopsis, IBA/IDA) - UniProtKB:Q9SVL1 At3g50880 (Arabidopsis, IBA) mechanism: IBA PANTHER:PTN002452908; IBA PANTHER:PTN001268735; IDA PMID:22532610 (GO_Central) verdict: FLAG_FAILS reason: ALKBH2 homolog IDA/IBA and 3-methyladenine glycosylase IBA (PTN002452908, seeded by yeast MAG1 and E. coli AlkA) describe conserved alkylation repair. - go_id: GO:0000096 label: sulfur amino acid metabolic process aspect: BP annotations: - UniProtKB:O49485 PGDH1 (Arabidopsis, IMP) - UniProtKB:O82796 PSP (Arabidopsis, IMP) mechanism: IMP PMID:30787133 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on PGDH1, PSP rest on full text not read here. - go_id: GO:0010636 label: positive regulation of mitochondrial fusion aspect: BP annotations: - UniProtKB:F4J5S1 FMT (Arabidopsis, IMP) mechanism: IMP PMID:25165398 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on FMT rest on full text not read here. - go_id: GO:0043515 label: kinetochore binding aspect: MF annotations: - UniProtKB:F4JT58 EMB3006 (Arabidopsis, IPI) mechanism: IPI PMID:34850467 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on EMB3006 rest on full text not read here. - go_id: GO:0051792 label: medium-chain fatty acid biosynthetic process aspect: BP annotations: - UniProtKB:Q9LNJ4 CYP703A2 (Arabidopsis, IDA) mechanism: IDA PMID:17496121 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CYP703A2 rest on full text not read here. - go_id: GO:2000234 label: positive regulation of rRNA processing aspect: BP annotations: - UniProtKB:Q9FR53 TOR (Arabidopsis, IMP) mechanism: IMP PMID:21266656 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on TOR rest on full text not read here. - go_id: GO:2000369 label: regulation of clathrin-dependent endocytosis aspect: BP annotations: - UniProtKB:Q9SIS4 IP5P9 (Arabidopsis, IMP) mechanism: IMP PMID:23658066 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on IP5P9 rest on full text not read here. - go_id: GO:0044843 label: cell cycle G1/S phase transition aspect: BP annotations: - UniProtKB:Q96327 EBP1 (Arabidopsis, IEP) mechanism: IEP PMID:15689342 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP row(s) from UniProt on EBP1 rest on full text not read here. - go_id: GO:0010513 label: positive regulation of phosphatidylinositol biosynthetic process aspect: BP annotations: - UniProtKB:Q94C26 PCC1 (Arabidopsis, IMP) mechanism: IMP PMID:23833195 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PCC1 rest on full text not read here. - go_id: GO:0016587 label: Isw1 complex aspect: CC annotations: - UniProtKB:Q9SFV2 FHA2 (Arabidopsis, IPI) mechanism: IPI PMID:32396248 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on FHA2 rest on full text not read here. - go_id: GO:0006216 label: cytidine catabolic process aspect: BP annotations: - UniProtKB:O65896 CDA1 (Arabidopsis, IMP) mechanism: IMP PMID:27208239 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CDA1 rest on full text not read here. - go_id: GO:0033044 label: regulation of chromosome organization aspect: BP annotations: - UniProtKB:Q9FKS4 ATR (Arabidopsis, IGI) - UniProtKB:Q9M3G7 ATM (Arabidopsis, IGI) mechanism: IGI PMID:16166376 (TAIR); IGI PMID:17989233 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on ATM, ATR rest on full text not read here. - go_id: GO:0046820 label: aminodeoxychorismate synthase activity aspect: MF annotations: - UniProtKB:D8QZ33 (Selaginella, IBA/IEA) - UniProtKB:Q8LPN3 ADCS (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN002599721; IEA EC:2.6.1.85; IEA UniProtKB:Q8LPN3; IDA PMID:20851095 (TAIR); IEA RHEA:11672; IEA ARBA:ARBA00084915 verdict: FLAG_FAILS reason: Plant ADCS (folate pathway) is a characterised aminodeoxychorismate synthase (IDA); the IBA, EC, RHEA and Ensembl rows agree. - go_id: GO:0140934 label: histone deubiquitinase activity aspect: MF annotations: - UniProtKB:Q9XIP2 OTU6 (Arabidopsis, IDA) mechanism: IDA PMID:21690391 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on OTU6 rest on full text not read here. - go_id: GO:0004418 label: hydroxymethylbilane synthase activity aspect: MF annotations: - UniProtKB:D8QTP5 (Selaginella, IBA/IEA) - UniProtKB:D8T3U1 (Selaginella, IBA/IEA) - UniProtKB:Q43316 HEMC (Arabidopsis, IBA/IDA/IEA/IMP) mechanism: IBA PANTHER:PTN000168159; IEA InterPro:IPR000860; IEA EC:2.5.1.61; IEA ARBA:ARBA00028611; IDA PMID:8192681 (TAIR); IEA RHEA:13185; IMP PMID:23308205 (TAIR) verdict: FLAG_FAILS reason: Porphobilinogen deaminase (HEMC) of tetrapyrrole synthesis; IDA, IMP, IBA and InterPro rows agree. - go_id: GO:0052856 label: NAD(P)HX epimerase activity aspect: MF annotations: - UniProtKB:D8R082 (Selaginella, IBA/IEA) - UniProtKB:D8SZQ0 (Selaginella, IBA/IEA) - UniProtKB:Q9LTX3 PPOX1 (Arabidopsis, IDA/IEA) mechanism: IBA PANTHER:PTN000325829; IEA EC:5.1.99.6; IEA UniRule:UR000375952; IEA RHEA:32215; IDA PMID:24599492 (TAIR); IEA InterPro:IPR021198 verdict: FLAG_FAILS reason: NAD(P)HX epimerase is a universal metabolite-repair enzyme; the Arabidopsis IDA and the IBA/UniRule rows agree. - go_id: GO:0003842 label: L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity aspect: MF annotations: - UniProtKB:D8RC17 (Selaginella, IBA) - UniProtKB:D8T2W4 (Selaginella, IBA) - UniProtKB:Q8VZC3 ALDH12A1 (Arabidopsis, IBA/IEA/IMP) mechanism: IBA PANTHER:PTN000192427; IEA EC:1.2.1.88; IMP PMID:11532180 (TAIR) verdict: FLAG_FAILS reason: P5CDH (proline catabolism) IMP, with an IBA seeded by itself; correct. - go_id: GO:0004152 label: dihydroorotate dehydrogenase activity aspect: MF annotations: - UniProtKB:D8R3V8 (Selaginella, IBA/IEA) - UniProtKB:D8RAG3 (Selaginella, IBA/IEA) - UniProtKB:P32746 PYRD (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN000234184; IEA InterPro:IPR005719; IEA UniProtKB:P32746; IEA ARBA:ARBA00047233; IDA PMID:12372626 (TAIR) verdict: FLAG_FAILS reason: Plant mitochondrial DHODH (PYRD) IDA, with conserved IBA and InterPro rows. - go_id: GO:0004413 label: homoserine kinase activity aspect: MF annotations: - UniProtKB:D8R3R1 (Selaginella, IEA) - UniProtKB:D8SIF2 (Selaginella, IEA) - UniProtKB:Q8L7R2 HSK (Arabidopsis, IDA/IEA) mechanism: IEA InterPro:IPR000870; IEA EC:2.7.1.39; IDA PMID:15703056 (TAIR); IEA RHEA:13985 verdict: FLAG_FAILS reason: Plant homoserine kinase IDA, with InterPro/EC rows; correct. - go_id: GO:0003855 label: 3-dehydroquinate dehydratase activity aspect: MF annotations: - UniProtKB:D8S7P3 (Selaginella, IEA) - UniProtKB:D8T411 (Selaginella, IEA) - UniProtKB:Q9SQT8 EMB3004 (Arabidopsis, EXP/IEA) mechanism: IEA InterPro:IPR001381; IEA ARBA:ARBA00027694; EXP PMID:16784230 (UniProt); IEA EC:4.2.1.10; IEA RHEA:21096 verdict: FLAG_FAILS reason: Plant DHQ-SDH is bifunctional; EXP plus InterPro/ARBA rows for 3-dehydroquinate dehydratase are right. - go_id: GO:0004764 label: shikimate 3-dehydrogenase (NADP+) activity aspect: MF annotations: - UniProtKB:D8S7P3 (Selaginella, IBA/IEA) - UniProtKB:D8T411 (Selaginella, IBA/IEA) - UniProtKB:Q9SQT8 EMB3004 (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN000472519; IEA InterPro:IPR011342; IEA EC:1.1.1.25; IDA PMID:16784230 (TAIR); IEA RHEA:17737 verdict: FLAG_FAILS reason: The same bifunctional DHQ-SDH, shikimate dehydrogenase domain (IDA, IBA, InterPro); correct. - go_id: GO:0008990 label: rRNA (guanine-N2-)-methyltransferase activity aspect: MF annotations: - UniProtKB:A0A1I9LP45 At3g28460 (Arabidopsis, IDA) - UniProtKB:A0A1I9LP46 At3g28460 (Arabidopsis, IDA) - UniProtKB:Q9LSI8 At3g28460 (Arabidopsis, IDA) mechanism: IDA PMID:34015128 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on At3g28460 rest on full text not read here. - go_id: GO:0005539 label: glycosaminoglycan binding aspect: MF annotations: - UniProtKB:Q9ZVA4 At1g78850 (Arabidopsis, IPI) mechanism: IPI PMID:30156702 (TAIR) verdict: ANNOTATION_WRONG reason: AtGAL1 (At1g78850) is a mannose-binding lectin. It co-purifies with AtPAP26 and is thought to bind that protein's high-mannose N-glycans, which are not glycosaminoglycans. Plants make no glycosaminoglycans, and an IPI with a protein partner does not show GAG binding. replacement: GO:0005537 D-mannose binding (candidate; the glycan binding is hypothesized in the paper, not shown) supported_by: - reference_id: PMID:30156702 supporting_text: We hypothesize that binding of AtPAP26-S2's high-mannose glycans by AtGAL1 enhances AtPAP26 function - go_id: GO:0045176 label: apical protein localization aspect: BP annotations: - UniProtKB:Q8H1D3 NPY1 (Arabidopsis, IGI) mechanism: IGI PMID:16107478 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on NPY1 rest on full text not read here. - go_id: GO:0005547 label: phosphatidylinositol-3,4,5-trisphosphate binding aspect: MF annotations: - UniProtKB:Q8VWF1 SH3P2 (Arabidopsis, IDA) - UniProtKB:Q96262 PCAP1 (Arabidopsis, IDA) - UniProtKB:Q9FG74 D6PK (Arabidopsis, IDA) mechanism: IDA PMID:28584166 (UniProt); IDA PMID:18397324 (TAIR); IDA PMID:18397324 (UniProt); IDA PMID:27251533 (UniProt) verdict: DEFER_TO_CURATOR reason: IDA lipid-overlay binding is accepted MF practice, but PI(3,4,5)P3 has not been detected in plants (no class I PI3K), so the binding is probably non-physiological; leave it to the curators. - go_id: GO:0007276 label: gamete generation aspect: BP annotations: - UniProtKB:F4IH25 BOP1 (Arabidopsis, IMP) - UniProtKB:Q38914 ANT (Arabidopsis, IMP) - UniProtKB:Q9ZRT1 GR1 (Arabidopsis, IMP) mechanism: IMP PMID:26940494 (TAIR); IMP PMID:8742706 (TIGR); IMP PMID:18007598 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/TIGR on ANT, BOP1, GR1 rest on full text not read here. - go_id: GO:0007097 label: nuclear migration aspect: BP annotations: - UniProtKB:O23702 AN (Arabidopsis, IMP) - UniProtKB:Q0WPU1 XI-I (Arabidopsis, IMP) - UniProtKB:Q5XVI1 SINE1 (Arabidopsis, IMP) mechanism: IMP PMID:30404821 (TAIR); IMP PMID:23973298 (UniProt); IMP PMID:24891605 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/UniProt on AN, SINE1, XI-I rest on full text not read here. - go_id: GO:0008494 label: translation activator activity aspect: MF annotations: - UniProtKB:D8QN31 (Selaginella, IBA) - UniProtKB:D8R709 (Selaginella, IBA) - UniProtKB:Q9SNB7 LPE1 (Arabidopsis, IBA/IMP) mechanism: IBA PANTHER:PTN005403777; IMP PMID:30844105 (TAIR) verdict: FLAG_FAILS reason: IBA PTN005403777 seeded by AT3G46610 itself plus its IMP; consistent. - go_id: GO:1902275 label: regulation of chromatin organization aspect: BP annotations: - UniProtKB:Q8LGE3 ARP6 (Arabidopsis, IPI) - UniProtKB:Q9FMT4 At5g14170 (Arabidopsis, IMP) - UniProtKB:Q9XIP2 OTU6 (Arabidopsis, IMP) mechanism: IPI PMID:35026437 (TAIR); IMP PMID:26457678 (UniProt); IMP PMID:27999174 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP/IPI row(s) from TAIR/UniProt on ARP6, At5g14170, OTU6 rest on full text not read here. - go_id: GO:2000232 label: regulation of rRNA processing aspect: BP annotations: - UniProtKB:F4JHU0 MAS2 (Arabidopsis, IMP) - UniProtKB:Q9LYK7 PES (Arabidopsis, IMP) mechanism: IMP PMID:26139346 (TAIR); IMP PMID:23909681 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on MAS2, PES rest on full text not read here. - go_id: GO:0005496 label: steroid binding aspect: MF annotations: - UniProtKB:O22476 BRI1 (Arabidopsis, IDA) - UniProtKB:Q9XFM6 MSBP1 (Arabidopsis, IDA) mechanism: IDA PMID:21666665 (TAIR); IDA PMID:15608331 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on BRI1, MSBP1 rest on full text not read here. - go_id: GO:0042177 label: negative regulation of protein catabolic process aspect: BP annotations: - UniProtKB:Q9C800 At1g33530 (Arabidopsis, IBA) - UniProtKB:Q9LZQ2 At3g62380 (Arabidopsis, IBA) - UniProtKB:Q9SU30 CPR1 (Arabidopsis, IBA/IMP) mechanism: IBA PANTHER:PTN008639574; IMP PMID:21967323 (TAIR) verdict: ANNOTATION_WRONG reason: The sign looks inverted. The cited paper (abstract only) shows CPR1 lowers SNC1 levels through 26S-proteasome degradation, so it promotes protein catabolism. The IBA (PTN008639574, seeded only by CPR1) copies the inverted sign to two other F-box proteins (At1g33530, At3g62380). replacement: GO:0045732 positive regulation of protein catabolic process supported_by: - reference_id: PMID:21967323 supporting_text: Here we report the identification of an F-box protein CPR1/CPR30 as a negative regulator of an R protein SNC1 likely through SCF (Skp1-cullin-F-box) mediated protein degradation. - go_id: GO:0034618 label: arginine binding aspect: MF annotations: - UniProtKB:Q9SCL7 NAGK (Arabidopsis, IDA) mechanism: IDA PMID:17913711 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on NAGK rest on full text not read here. - go_id: GO:0015173 label: aromatic amino acid transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9FKY3 AVT3A (Arabidopsis, IDA) - UniProtKB:Q9SF09 ANT1 (Arabidopsis, IMP) mechanism: IDA PMID:27925655 (UniProt); IMP PMID:11299361 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR/UniProt on ANT1, AVT3A rest on full text not read here. - go_id: GO:0008782 label: adenosylhomocysteine nucleosidase activity aspect: MF annotations: - UniProtKB:Q7XA67 MTN2 (Arabidopsis, EXP/IEA) mechanism: EXP PMID:18342331 (UniProt); EXP PMID:19249293 (UniProt); IEA EC:3.2.2.9; IEA RHEA:17805 verdict: FLAG_FAILS reason: Plant MTN (methylthioadenosine/SAH nucleosidase) EXP, with EC/RHEA IEA; correct. - go_id: GO:0005432 label: calcium:sodium antiporter activity aspect: MF annotations: - UniProtKB:Q8L636 NCL (Arabidopsis, IDA) mechanism: IDA PMID:23148213 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on NCL rest on full text not read here. - go_id: GO:0040014 label: regulation of multicellular organism growth aspect: BP annotations: - UniProtKB:P31265 TCTP1 (Arabidopsis, IMP) - UniProtKB:Q8RVL2 DEK1 (Arabidopsis, IMP) mechanism: IMP PMID:20736351 (TAIR); IMP PMID:18952779 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on DEK1, TCTP1 rest on full text not read here. - go_id: GO:0010888 label: negative regulation of lipid storage aspect: BP annotations: - UniProtKB:O81270 PXG1 (Arabidopsis, IMP) mechanism: IMP PMID:16961733 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PXG1 rest on full text not read here. - go_id: GO:0039694 label: viral RNA genome replication aspect: BP annotations: - UniProtKB:Q9LUW6 RH9 (Arabidopsis, IMP) mechanism: IMP PMID:27456972 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on RH9 rest on full text not read here. - go_id: GO:0097708 label: intracellular vesicle aspect: CC annotations: - UniProtKB:Q8S8K8 CV (Arabidopsis, IBA/IDA) - UniProtKB:Q9SX20 NPF3.1 (Arabidopsis, IDA) mechanism: IBA PANTHER:PTN002202256; IDA PMID:25538186 (TAIR); IDA PMID:27139299 (TAIR) verdict: FLAG_FAILS reason: Generic vesicle location; the IDA and the IBA seeded by the same Arabidopsis locus agree. - go_id: GO:0032794 label: GTPase activating protein binding aspect: MF annotations: - UniProtKB:P92978 ARAC11 (Arabidopsis, IPI) mechanism: IPI PMID:19108776 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on ARAC11 rest on full text not read here. - go_id: GO:0051290 label: protein heterotetramerization aspect: BP annotations: - UniProtKB:O65282 CPN20 (Arabidopsis, IPI) mechanism: IPI PMID:23783410 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from UniProt on CPN20 rest on full text not read here. - go_id: GO:0043394 label: proteoglycan binding aspect: MF annotations: - UniProtKB:O81865 PP2A1 (Arabidopsis, IDA) mechanism: IDA PMID:20442276 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PP2A1 rest on full text not read here. - go_id: GO:0070509 label: calcium ion import aspect: BP annotations: - UniProtKB:O65718 CNGC2 (Arabidopsis, IDA) - UniProtKB:Q9LVR5 MCU6 (Arabidopsis, IMP) mechanism: IDA PMID:27999084 (TAIR); IMP PMID:31182842 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR on CNGC2, MCU6 rest on full text not read here. - go_id: GO:0010867 label: positive regulation of triglyceride biosynthetic process aspect: BP annotations: - UniProtKB:Q9FLT5 ABCA9 (Arabidopsis, IMP) mechanism: IMP PMID:23269834 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on ABCA9 rest on full text not read here. - go_id: GO:0048311 label: mitochondrion distribution aspect: BP annotations: - UniProtKB:Q6NNL9 NOXY2 (Arabidopsis, IMP) mechanism: IMP PMID:23370715 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on NOXY2 rest on full text not read here. - go_id: GO:0042554 label: superoxide anion generation aspect: BP annotations: - UniProtKB:Q8GUQ8 XDH1 (Arabidopsis, IMP) mechanism: IMP PMID:15941399 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on XDH1 rest on full text not read here. - go_id: GO:0007088 label: regulation of mitotic nuclear division aspect: BP annotations: - UniProtKB:O48533 PYM (Arabidopsis, IBA) - UniProtKB:Q9M2R1 GIG1 (Arabidopsis, IBA/IMP) mechanism: IBA PANTHER:PTN008666874; IMP PMID:22167058 (TAIR) verdict: FLAG_FAILS reason: IBA seeded by AT3G57860 (GIG1/OSD1, APC/C inhibitor) plus IMP; conserved regulation of mitosis. - go_id: GO:0003939 label: L-iditol 2-dehydrogenase (NAD+) activity aspect: MF annotations: - UniProtKB:Q9FJ95 SDH (Arabidopsis, EXP/IDA/IEA) mechanism: EXP PMID:23498864 (UniProt); IDA DOI:10.1016/j.plantsci.2013.01.012 (UniProt); IEA RHEA:33031 verdict: FLAG_FAILS reason: Arabidopsis sorbitol dehydrogenase (EXP/IDA) with a RHEA IEA; correct. - go_id: GO:0046526 label: D-xylulose reductase activity aspect: MF annotations: - UniProtKB:Q9FJ95 SDH (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN001707508; IDA PMID:23498864 (TAIR); IEA EC:1.1.1.9; IEA RHEA:20433 verdict: FLAG_FAILS reason: The same SDH enzyme with xylitol/xylulose activity (IDA); IBA seeded by itself. - go_id: GO:0010845 label: positive regulation of reciprocal meiotic recombination aspect: BP annotations: - UniProtKB:F4IDW9 PTD (Arabidopsis, IMP) mechanism: IMP PMID:24656236 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on PTD rest on full text not read here. - go_id: GO:0052642 label: lysophosphatidic acid phosphatase activity aspect: MF annotations: - UniProtKB:Q9SRQ6 NPC3 (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN008642411; IDA PMID:20045079 (TAIR); IEA EC:3.1.3.106; IEA RHEA:33155 verdict: FLAG_FAILS reason: Lysophosphatidic acid phosphatase IDA, with an IBA seeded by itself and EC/RHEA rows; consistent. - go_id: GO:0016247 label: channel regulator activity aspect: MF annotations: - UniProtKB:P18064 GPA1 (Arabidopsis, IMP) mechanism: IMP PMID:11408655 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on GPA1 rest on full text not read here. - go_id: GO:0032197 label: retrotransposition aspect: BP annotations: - UniProtKB:Q9XFH4 DDM1 (Arabidopsis, IMP) mechanism: IMP PMID:19734880 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on DDM1 rest on full text not read here. - go_id: GO:0046337 label: phosphatidylethanolamine metabolic process aspect: BP annotations: - UniProtKB:Q9C6B9 NMT3 (Arabidopsis, IDA) mechanism: IDA PMID:29777000 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on NMT3 rest on full text not read here. - go_id: GO:0015247 label: aminophospholipid flippase activity aspect: MF annotations: - UniProtKB:Q9XIE6 ALA3 (Arabidopsis, IDA/IMP) mechanism: IDA PMID:18344284 (TAIR); IMP PMID:32817253 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR on ALA3 rest on full text not read here. - go_id: GO:0033597 label: mitotic checkpoint complex aspect: CC annotations: - UniProtKB:Q9S7I8 CDC20-2 (Arabidopsis, IPI) - UniProtKB:Q9SZA4 CDC20-1 (Arabidopsis, IPI) mechanism: IPI PMID:21687678 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on CDC20-1, CDC20-2 rest on full text not read here. - go_id: GO:1900103 label: positive regulation of endoplasmic reticulum unfolded protein response aspect: BP annotations: - UniProtKB:Q9SCK6 NAC062 (Arabidopsis, IMP) mechanism: IMP PMID:24961665 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on NAC062 rest on full text not read here. - go_id: GO:0110152 label: RNA NAD+-cap (NAD+-forming) hydrolase activity aspect: MF annotations: - UniProtKB:Q8RY73 DXO1 (Arabidopsis, EXP/IEA) mechanism: EXP PMID:30949699 (UniProt); IEA RHEA:60880 verdict: FLAG_FAILS reason: DXO1 NAD+-cap decapping (EXP) with RHEA IEA; plant DXO1 is a characterised deNADding enzyme. - go_id: GO:0080007 label: S-nitrosoglutathione reductase (NADH) activity aspect: MF annotations: - UniProtKB:Q96533 ADH2 (Arabidopsis, EXP/IEA/IMP) mechanism: EXP PMID:38308388 (UniProt); IEA RHEA:78371; IMP PMID:18326829 (TAIR) verdict: FLAG_FAILS reason: GSNOR1 (HOT5/PAR2) is the plant S-nitrosoglutathione reductase (EXP/IMP); correct. - go_id: GO:0033721 label: aldehyde dehydrogenase (NADP+) activity aspect: MF annotations: - UniProtKB:Q8W033 ALDH3I1 (Arabidopsis, IDA) mechanism: IDA PMID:21166653 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on ALDH3I1 rest on full text not read here. - go_id: GO:0004059 label: aralkylamine N-acetyltransferase activity aspect: MF annotations: - UniProtKB:Q7X9V3 NSI (Arabidopsis, IDA/IEA) - UniProtKB:Q9C666 SNAT2 (Arabidopsis, IDA/IEA) mechanism: IDA PMID:25250906 (TAIR); IEA EC:2.3.1.87; IEA UniProtKB:Q5KQI6; IEA RHEA:66144; IDA PMID:31698875 (UniProt) verdict: FLAG_FAILS reason: Plant serotonin N-acetyltransferases (SNAT) make melatonin (IDA); the EC/RHEA and rice projection IEA rows agree. - go_id: GO:0015805 label: S-adenosyl-L-methionine transport aspect: BP annotations: - UniProtKB:Q94AG6 SAMC1 (Arabidopsis, IDA) mechanism: IDA PMID:17098813 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SAMC1 rest on full text not read here. - go_id: GO:0004741 label: '[pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity' aspect: MF annotations: - UniProtKB:O81760 PP2C63 (Arabidopsis, IDA) mechanism: IDA PMID:33798747 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PP2C63 rest on full text not read here. - go_id: GO:1903754 label: cortical microtubule plus-end aspect: CC annotations: - UniProtKB:Q9MA92 FPP3 (Arabidopsis, IDA) - UniProtKB:Q9SFF4 FPP2 (Arabidopsis, IDA) mechanism: IDA PMID:25541219 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on FPP2, FPP3 rest on full text not read here. - go_id: GO:0060211 label: regulation of nuclear-transcribed mRNA poly(A) tail shortening aspect: BP annotations: - UniProtKB:O64380 PAB3 (Arabidopsis, IDA) - UniProtKB:P42731 PAB2 (Arabidopsis, IDA) mechanism: IDA PMID:14624004 (UniProt); IDA PMID:10849337 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on PAB2, PAB3 rest on full text not read here. - go_id: GO:0047434 label: indolepyruvate decarboxylase activity aspect: MF annotations: - UniProtKB:Q9LFM5 YUC4 (Arabidopsis, IDA) mechanism: IDA PMID:22233288 (TAIR) verdict: ANNOTATION_WRONG reason: Indolepyruvate decarboxylase makes indole-3-acetaldehyde, which is the bacterial route. YUC4 is a flavin monooxygenase that turns indole-3-pyruvate straight into IAA. The cited paper reports only isoform localisation. replacement: GO:0103075 indole-3-pyruvate monooxygenase activity supported_by: - reference_id: PMID:22233288 supporting_text: YUCCA family of flavin-dependent mono-oxygenases - go_id: GO:2000185 label: regulation of phosphate transmembrane transport aspect: BP annotations: - UniProtKB:Q8VY10 UBC24 (Arabidopsis, IGI) mechanism: IGI PMID:24122829 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on UBC24 rest on full text not read here. - go_id: GO:0006825 label: copper ion transport aspect: BP annotations: - UniProtKB:B9DFX7 PAA2 (Arabidopsis, IMP) - UniProtKB:Q39065 COPT1 (Arabidopsis, IGI) - UniProtKB:Q94FT1 COX17-2 (Arabidopsis, IDA) mechanism: IMP PMID:15772282 (TAIR); IGI PMID:7499355 (TAIR); IDA PMID:12196180 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IGI/IMP row(s) from TAIR on COPT1, COX17-2, PAA2 rest on full text not read here. - go_id: GO:0043254 label: regulation of protein-containing complex assembly aspect: BP annotations: - UniProtKB:P92973 CCA1 (Arabidopsis, IMP) - UniProtKB:Q9FFA7 RUP2 (Arabidopsis, IDA/IEA) - UniProtKB:Q9LTJ6 RUP1 (Arabidopsis, IDA/IEA) mechanism: IMP PMID:20007447 (TAIR); IDA PMID:23277547 (TAIR); IEA ARBA:ARBA00086482 verdict: FLAG_FAILS reason: RUP1/RUP2 drive UVR8 redimerisation (IDA), so the ARBA IEA rows are right; P92973 IMP plausible. - go_id: GO:0031334 label: positive regulation of protein-containing complex assembly aspect: BP annotations: - UniProtKB:F4J1U2 BFA1 (Arabidopsis, IMP) - UniProtKB:F4J2Z0 BFA1 (Arabidopsis, IMP) - UniProtKB:F4K2E9 CUV (Arabidopsis, IGI) mechanism: IMP PMID:30012777 (TAIR); IGI PMID:25902521 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IMP row(s) from TAIR on BFA1, CUV rest on full text not read here. - go_id: GO:0045792 label: negative regulation of cell size aspect: BP annotations: - UniProtKB:F4IME8 NAC036 (Arabidopsis, IMP) mechanism: IMP PMID:19962211 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on NAC036 rest on full text not read here. - go_id: GO:0047661 label: amino-acid racemase activity aspect: MF annotations: - UniProtKB:F4JHW0 DAAR1 (Arabidopsis, IDA) mechanism: IDA PMID:26324904 (TAIR) verdict: DEFER_TO_CURATOR reason: DAAR1 (PhzF family) amino-acid racemase IDA; plants have D-amino-acid metabolism, full text not read. - go_id: GO:0047661 label: amino-acid racemase activity aspect: MF annotations: - UniProtKB:D8SNH7 (Selaginella, IBA) - UniProtKB:Q9XI28 At1g15410 (Arabidopsis, IBA/IEA) mechanism: IBA PANTHER:PTN002722431; IEA InterPro:IPR015942; IEA ARBA:ARBA00029237 verdict: UNCERTAIN reason: PTN002722431 is seeded by bacterial glutamate racemases (MurI) and propagates to plant Asp/Glu-racemase family proteins of unknown function. IPR015942 also covers hydantoin racemases and maleate isomerases. Settled by an enzyme assay on Q9XI28. - go_id: GO:0019305 label: dTDP-rhamnose biosynthetic process aspect: BP annotations: - UniProtKB:Q9LQ04 NRS/ER (Arabidopsis, IDA) mechanism: IDA PMID:15020741 (TAIR) verdict: DEFER_TO_CURATOR reason: NRS/ER converts dTDP-4-keto-6-deoxy-Glc to dTDP-rhamnose in vitro (Watt 2004); the IDA is sound as measured. - go_id: GO:0019305 label: dTDP-rhamnose biosynthetic process aspect: BP annotations: - UniProtKB:D8R443 (Selaginella, IBA) - UniProtKB:Q9LQ04 NRS/ER (Arabidopsis, IBA/IEA) mechanism: IBA PANTHER:PTN002233786; IEA UniProtKB-UniPathway:UPA00124 verdict: UNCERTAIN reason: The IBA (PTN002233786, seeded only by NRS/ER) and the UniPathway IEA carry an in vitro dTDP result into a plant process. Plants make UDP-rhamnose for pectin and glycosides, and the same enzyme also forms UDP-rhamnose. Settled by evidence that plants make dTDP-rhamnose in vivo; otherwise GO:0010253 UDP-rhamnose biosynthetic process is the better propagated term. - go_id: GO:0019305 label: dTDP-rhamnose biosynthetic process aspect: BP annotations: - UniProtKB:Q9LZI2 UXS2 (Arabidopsis, ISS) mechanism: ISS from PMID:11554483 verdict: ANNOTATION_WRONG reason: UXS2 is UDP-glucuronate decarboxylase (UDP-xylose synthase) per UniProt. The ISS probably followed its old name "dTDP-glucose 4-6-dehydratase homolog D18" and is the wrong family member for rhamnose synthesis. replacement: GO:0033320 UDP-D-xylose biosynthetic process - go_id: GO:0019236 label: response to pheromone aspect: BP annotations: - UniProtKB:P18064 GPA1 (Arabidopsis, IMP) - UniProtKB:Q94AH1 CAND2 (Arabidopsis, IEP/IMP) mechanism: IMP PMID:29702752 (UniProt); IEP PMID:29702752 (UniProt) verdict: ANNOTATION_WRONG reason: The paper is about melatonin, which it calls a putative phytohormone; a pheromone is a signal between individuals of one species. The CAND2/PMTR1 and GPA1 rows describe melatonin-induced stomatal closure. GO has no "response to melatonin" term (an ontology gap). replacement: GO:0090332 stomatal closure (assayed phenotype); propose a response-to-melatonin term supported_by: - reference_id: PMID:29702752 supporting_text: Here, we discovered the first phytomelatonin receptor (CAND2/PMTR1) in Arabidopsis thaliana and found that melatonin governs the receptor-dependent stomatal closure. - go_id: GO:0051019 label: mitogen-activated protein kinase binding aspect: MF annotations: - UniProtKB:Q9FJV0 MKK6 (Arabidopsis, IPI) - UniProtKB:Q9MA75 VIP1 (Arabidopsis, IPI) mechanism: IPI PMID:30185442 (TAIR); IPI PMID:17947581 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR/UniProt on MKK6, VIP1 rest on full text not read here. - go_id: GO:0045806 label: negative regulation of endocytosis aspect: BP annotations: - UniProtKB:Q0WQ57 At4g12770 (Arabidopsis, IDA/IMP) - UniProtKB:Q9SU08 AUXI1 (Arabidopsis, IDA) mechanism: IDA PMID:29511054 (TAIR); IMP PMID:29511054 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IMP row(s) from TAIR on AUXI1, At4g12770 rest on full text not read here. - go_id: GO:0034705 label: potassium channel complex aspect: CC annotations: - UniProtKB:Q9SVV6 TPK3 (Arabidopsis, IDA) mechanism: IDA PMID:31201323 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on TPK3 rest on full text not read here. - go_id: GO:0034595 label: phosphatidylinositol phosphate 5-phosphatase activity aspect: MF annotations: - UniProtKB:Q9SIS4 IP5P9 (Arabidopsis, IDA) mechanism: IDA PMID:23658066 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on IP5P9 rest on full text not read here. - go_id: GO:0040015 label: negative regulation of multicellular organism growth aspect: BP annotations: - UniProtKB:Q9LFS4 CIK5 (Arabidopsis, IMP) mechanism: IMP PMID:19112492 (CAFA) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from CAFA on CIK5 rest on full text not read here. - go_id: GO:0006986 label: response to unfolded protein aspect: BP annotations: - UniProtKB:D8S2V7 (Selaginella, IEA) - UniProtKB:D8S8C5 (Selaginella, IEA) - UniProtKB:Q9SG86 BZIP28 (Arabidopsis, IMP) mechanism: IEA ARBA:ARBA00086617; IMP PMID:18156219 (TAIR) verdict: FLAG_FAILS reason: Generic stress term; IMP on Arabidopsis and ARBA IEA on Selaginella homologs are plausible. - go_id: GO:0010520 label: regulation of reciprocal meiotic recombination aspect: BP annotations: - UniProtKB:P16128 At4g18490 (Arabidopsis, IMP) - UniProtKB:Q8GW48 HSBP (Arabidopsis, IMP) - UniProtKB:Q9FGW5 CDKG1 (Arabidopsis, IMP) mechanism: IMP PMID:41254312 (TAIR); IMP PMID:35670129 (TAIR); IMP PMID:32047050 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on At4g18490, CDKG1, HSBP rest on full text not read here. - go_id: GO:0008154 label: actin polymerization or depolymerization aspect: BP annotations: - UniProtKB:Q42418 PRF2 (Arabidopsis, IDA) - UniProtKB:Q42449 PRF1 (Arabidopsis, IDA) mechanism: IDA PMID:8647830 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PRF1, PRF2 rest on full text not read here. - go_id: GO:0045948 label: positive regulation of translational initiation aspect: BP annotations: - UniProtKB:A8MR55 EDA35 (Arabidopsis, IMP) - UniProtKB:Q9C5Z2 TIF3H1 (Arabidopsis, IMP) - UniProtKB:Q9M0V1 EDA35 (Arabidopsis, IMP) mechanism: IMP PMID:36801014 (TAIR); IMP PMID:15548739 (UniProt); IMP PMID:23524850 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR/UniProt on EDA35, TIF3H1 rest on full text not read here. - go_id: GO:0045022 label: early endosome to late endosome transport aspect: BP annotations: - UniProtKB:D8S6P2 (Selaginella, IBA) - UniProtKB:F4IJ68 At2g46560 (Arabidopsis, IBA) - UniProtKB:Q9CB01 RABF1 (Arabidopsis, IMP) mechanism: IBA PANTHER:PTN001193267; IBA PANTHER:PTN000359150; IMP PMID:11532937 (TAIR) verdict: FLAG_FAILS reason: Endosome maturation is conserved; IMP plus IBA nodes (seeded by VARP, Q96NW4, and yeast RAV1) are plausible. - go_id: GO:0004515 label: nicotinate-nucleotide adenylyltransferase activity aspect: MF annotations: - UniProtKB:D8QTW4 (Selaginella, IBA/IEA) - UniProtKB:F4K687 NMNAT (Arabidopsis, IBA/IDA/IEA/ISS) mechanism: IBA PANTHER:PTN000247701; IEA EC:2.7.7.18; IDA PMID:17270012 (TAIR); IEA InterPro:IPR045094; IEA RHEA:22860; ISS from UniProtKB:Q9HAN9 verdict: FLAG_FAILS reason: Plant NMNAT (NAD biosynthesis) IDA, with IBA/EC/RHEA/ISS rows; correct. - go_id: GO:0019200 label: carbohydrate kinase activity aspect: MF annotations: - UniProtKB:Q6ZY51 GWD3 (Arabidopsis, IDA) mechanism: IDA PMID:15686522 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on GWD3 rest on full text not read here. - go_id: GO:0050355 label: inorganic triphosphate phosphatase activity aspect: MF annotations: - UniProtKB:Q9SIY3 TTM3 (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN001842862; IDA PMID:24004165 (TAIR); IDA PMID:24004165 (UniProt); IEA EC:3.6.1.25; IEA RHEA:14157 verdict: FLAG_FAILS reason: Arabidopsis CYTH-domain triphosphate tunnel metalloenzyme (TTM3) hydrolyses PPPi (IDA); IBA seeded by itself. - go_id: GO:1903810 label: L-histidine import across plasma membrane aspect: BP annotations: - UniProtKB:Q9FKS8 LHT1 (Arabidopsis, IDA) mechanism: IDA PMID:9390441 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on LHT1 rest on full text not read here. - go_id: GO:0042882 label: L-arabinose transmembrane transport aspect: BP annotations: - UniProtKB:O04249 STP7 (Arabidopsis, IDA) mechanism: IDA PMID:29311272 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on STP7 rest on full text not read here. - go_id: GO:1903805 label: L-valine import across plasma membrane aspect: BP annotations: - UniProtKB:Q84MA5 CAT1 (Arabidopsis, IDA) mechanism: IDA PMID:8618839 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CAT1 rest on full text not read here. - go_id: GO:0004808 label: tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity aspect: MF annotations: - UniProtKB:Q8GUP2 At1g16445 (Arabidopsis, EXP/IEA) mechanism: EXP PMID:36762482 (UniProt); IEA EC:2.1.1.61 verdict: FLAG_FAILS reason: Plant tRNA mnm5s2U methyltransferase (EXP) with EC IEA; correct. - go_id: GO:0030638 label: polyketide metabolic process aspect: BP annotations: - UniProtKB:Q9LK50 ABCG26 (Arabidopsis, IMP) mechanism: IMP PMID:25415974 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on ABCG26 rest on full text not read here. - go_id: GO:0001881 label: receptor recycling aspect: BP annotations: - UniProtKB:Q9STT2 VPS29 (Arabidopsis, IDA) mechanism: IDA PMID:23263768 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on VPS29 rest on full text not read here. - go_id: GO:0003376 label: sphingosine-1-phosphate receptor signaling pathway aspect: BP annotations: - UniProtKB:P18064 GPA1 (Arabidopsis, IMP) mechanism: IMP PMID:12789341 (TAIR) verdict: DEFER_TO_CURATOR reason: S1P signalling in guard cells needs GPA1, but no plant S1P GPCR is known, while the term presupposes one; the curator chose it from full text not read. - go_id: GO:0070935 label: 3'-UTR-mediated mRNA stabilization aspect: BP annotations: - UniProtKB:A0A1P8AXB9 SRP1 (Arabidopsis, IDA) - UniProtKB:Q8S8K1 SRP1 (Arabidopsis, IDA) mechanism: IDA PMID:28174577 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on SRP1 rest on full text not read here. - go_id: GO:0071243 label: cellular response to arsenic-containing substance aspect: BP annotations: - UniProtKB:A0A1P8BC92 MYB40 (Arabidopsis, IDA) - UniProtKB:F4K6R6 MYB40 (Arabidopsis, IDA) mechanism: IDA PMID:34778748 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on MYB40 rest on full text not read here. - go_id: GO:0017064 label: fatty acid amide hydrolase activity aspect: MF annotations: - UniProtKB:Q7XJJ7 FAAH (Arabidopsis, EXP/IEA) mechanism: EXP PMID:12824167 (UniProt); IEA EC:3.5.1.99; IEA RHEA:26136 verdict: FLAG_FAILS reason: AtFAAH hydrolyses N-acylethanolamines (EXP); EC/RHEA rows agree. - go_id: GO:0098754 label: detoxification aspect: BP annotations: - UniProtKB:Q9ZQ94 UGT73C5 (Arabidopsis, IDA) mechanism: IDA PMID:12970342 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on UGT73C5 rest on full text not read here. - go_id: GO:0044020 label: histone H4R3 methyltransferase activity aspect: MF annotations: - UniProtKB:Q9MAT5 PRMT10 (Arabidopsis, IDA) mechanism: IDA PMID:18007657 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on PRMT10 rest on full text not read here. - go_id: GO:0140318 label: protein transporter activity aspect: MF annotations: - UniProtKB:Q93Z75 UPS5 (Arabidopsis, IMP) mechanism: IMP PMID:31862838 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on UPS5 rest on full text not read here. - go_id: GO:0140684 label: histone H3K9me2/H3K9me3 demethylase activity aspect: MF annotations: - UniProtKB:Q8RWR1 JMJ30 (Arabidopsis, IMP) mechanism: IMP PMID:29923261 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on JMJ30 rest on full text not read here. - go_id: GO:0071360 label: cellular response to exogenous dsRNA aspect: BP annotations: - UniProtKB:Q9SIW2 DRD1 (Arabidopsis, IMP) mechanism: IMP PMID:21771120 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on DRD1 rest on full text not read here. - go_id: GO:0043425 label: bHLH transcription factor binding aspect: MF annotations: - UniProtKB:O49687 MYC4 (Arabidopsis, IPI) - UniProtKB:Q9FIP9 MYC3 (Arabidopsis, IPI) - UniProtKB:Q9ZPW3 HBI1 (Arabidopsis, IDA) mechanism: IPI PMID:21335373 (TAIR); IDA PMID:23221598 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA/IPI row(s) from TAIR on HBI1, MYC3, MYC4 rest on full text not read here. - go_id: GO:0008395 label: steroid hydroxylase activity aspect: MF annotations: - UniProtKB:O48786 CYP734A1 (Arabidopsis, IBA/IMP) - UniProtKB:Q9M066 CYP90C1 (Arabidopsis, TAS) mechanism: IBA PANTHER:PTN001957721; IMP PMID:10611382 (TAIR); TAS PMID:9694802 (TIGR) verdict: FLAG_FAILS reason: CYP734A1/BAS1 (brassinosteroid C-26 hydroxylase; IMP, IBA seeded by itself) and CYP90C1 (TAS) are bona fide plant steroid hydroxylases. - go_id: GO:0035102 label: PRC1 complex aspect: CC annotations: - UniProtKB:Q0WX00 RING1B (Arabidopsis, IBA/IPI) - UniProtKB:Q94K49 ALP1 (Arabidopsis, IBA/IMP) - UniProtKB:Q9FKW0 RING1A (Arabidopsis, IBA/IPI) mechanism: IBA PANTHER:PTN001652016; IPI PMID:19097900 (TAIR); IPI PMID:19097900 (UniProt); IBA PANTHER:PTN002505681; IMP PMID:22837357 (UniProt); IMP PMID:26642436 (UniProt) verdict: FLAG_FAILS reason: Plant PRC1 (AtRING1b with BMI1 partners) is established; the ALP1 IMP/IBA rows (IBA seeded by ALP1 itself) are a curator call on a PcG-associated protein. - go_id: GO:0004698 label: calcium,diacylglycerol-dependent serine/threonine kinase activity aspect: MF annotations: - UniProtKB:Q6NLQ6 CPK32 (Arabidopsis, IDA) mechanism: IDA PMID:16299177 (TAIR) verdict: ANNOTATION_WRONG reason: The term is conventional PKC activity (activated by Ca2+ and diacylglycerol). CPK32 is a CDPK with a calmodulin-like domain and no DAG-binding C1 domain, and the paper never mentions diacylglycerol. replacement: GO:0009931 calcium-dependent protein serine/threonine kinase activity supported_by: - reference_id: PMID:16299177 supporting_text: Here we show that a calcium-dependent protein kinase is involved in the ABA-dependent activation process. - go_id: GO:0008476 label: protein-tyrosine sulfotransferase activity aspect: MF annotations: - UniProtKB:Q3EDG5 TPST (Arabidopsis, IDA/IEA) mechanism: IDA PMID:19666544 (TAIR); IEA EC:2.8.2.20; IEA RHEA:16801 verdict: FLAG_FAILS reason: AtTPST is the plant protein-tyrosine sulfotransferase (IDA), with EC/RHEA IEA; correct. - go_id: GO:0045839 label: negative regulation of mitotic nuclear division aspect: BP annotations: - UniProtKB:Q9LZ78 SIM (Arabidopsis, IMP) mechanism: IMP PMID:17098811 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on SIM rest on full text not read here. - go_id: GO:0071480 label: cellular response to gamma radiation aspect: BP annotations: - UniProtKB:Q0PCS3 CHR25 (Arabidopsis, IEP) - UniProtKB:Q8RXD4 BRCA1 (Arabidopsis, IEP) mechanism: IEP PMID:17227544 (UniProt); IEP PMID:16957774 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP row(s) from UniProt on BRCA1, CHR25 rest on full text not read here. - go_id: GO:0140104 label: molecular carrier activity aspect: MF annotations: - UniProtKB:O80493 DMP8 (Arabidopsis, IGI/IPI) - UniProtKB:Q9FK96 DMP9 (Arabidopsis, IGI/IPI) mechanism: IGI PMID:36322734 (TAIR); IPI PMID:36322734 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IPI row(s) from TAIR on DMP8, DMP9 rest on full text not read here. - go_id: GO:1902459 label: positive regulation of stem cell population maintenance aspect: BP annotations: - UniProtKB:O22446 HDA19 (Arabidopsis, IGI) - UniProtKB:Q8H1D2 WOX5 (Arabidopsis, IMP) mechanism: IGI PMID:26028217 (TAIR); IMP PMID:26028217 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IMP row(s) from TAIR on HDA19, WOX5 rest on full text not read here. - go_id: GO:0043269 label: regulation of monoatomic ion transport aspect: BP annotations: - UniProtKB:Q9M8U1 CML18 (Arabidopsis, IDA) mechanism: IDA PMID:16249341 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on CML18 rest on full text not read here. - go_id: GO:1902751 label: positive regulation of cell cycle G2/M phase transition aspect: BP annotations: - UniProtKB:C8KI33 SUV2 (Arabidopsis, IMP) mechanism: IMP PMID:19619159 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on SUV2 rest on full text not read here. - go_id: GO:0019217 label: regulation of fatty acid metabolic process aspect: BP annotations: - UniProtKB:Q9ZVH7 FAX3 (Arabidopsis, IMP) mechanism: IMP PMID:31198959 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on FAX3 rest on full text not read here. - go_id: GO:0045178 label: basal part of cell aspect: CC annotations: - UniProtKB:Q9FG74 D6PK (Arabidopsis, IDA) - UniProtKB:Q9LU77 PIN2 (Arabidopsis, IDA) mechanism: IDA PMID:33705718 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on D6PK, PIN2 rest on full text not read here. - go_id: GO:0022849 label: glutamate-gated calcium ion channel activity aspect: MF annotations: - UniProtKB:Q9C8E7 GLR3.3 (Arabidopsis, IMP) mechanism: IMP PMID:36796359 (TAIR) verdict: CONSTRAINT_QUESTIONABLE reason: The row breaks only_in_taxon Metazoa, but plant GLRs are glutamate-gated cation channels that conduct Ca2+ (GLR3.3 mediates wound-induced Ca2+ signalling). The biology looks right; the constraint should be widened to cover Viridiplantae. - go_id: GO:0061760 label: antifungal innate immune response aspect: BP annotations: - UniProtKB:Q9SQR5 SINE2 (Arabidopsis, IMP) mechanism: IMP PMID:24891605 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on SINE2 rest on full text not read here. - go_id: GO:0097237 label: cellular response to toxic substance aspect: BP annotations: - UniProtKB:Q9FFF6 JOX2 (Arabidopsis, IMP) mechanism: IMP PMID:27637093 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on JOX2 rest on full text not read here. - go_id: GO:0017145 label: stem cell division aspect: BP annotations: - UniProtKB:O65020 ETO1 (Arabidopsis, IMP) mechanism: IMP PMID:17656722 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on ETO1 rest on full text not read here. - go_id: GO:0052815 label: medium-chain fatty acyl-CoA hydrolase activity aspect: MF annotations: - UniProtKB:F4HU51 ACH2 (Arabidopsis, IDA) - UniProtKB:Q5FYU1 CNTE1 (Arabidopsis, ISS) mechanism: IDA PMID:14660652 (UniProt); ISS from UniProtKB:F4HU51 verdict: FLAG_FAILS reason: Same thioesterase pair as GO:0052816 (IDA plus paralog ISS); correct. - go_id: GO:0008281 label: sulfonylurea receptor activity aspect: MF annotations: - UniProtKB:Q7GB25 ABCC5 (Arabidopsis, IDA) mechanism: IDA PMID:14684837 (TAIR) verdict: DEFER_TO_CURATOR reason: AtMRP5/ABCC5 mediates glibenclamide (sulfonylurea) sensitivity; the term can apply, full text not read. - go_id: GO:0045859 label: regulation of protein kinase activity aspect: BP annotations: - UniProtKB:Q9SCY5 KINB2 (Arabidopsis, IPI) mechanism: IPI PMID:25736509 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IPI row(s) from TAIR on KINB2 rest on full text not read here. - go_id: GO:0036449 label: microtubule minus-end aspect: CC annotations: - UniProtKB:F4IIM1 CSI1 (Arabidopsis, IDA) mechanism: IDA PMID:22294619 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from UniProt on CSI1 rest on full text not read here. - go_id: GO:0048863 label: stem cell differentiation aspect: BP annotations: - UniProtKB:Q07100 PP2A3 (Arabidopsis, IGI/IMP) - UniProtKB:Q8L9H6 CLE17 (Arabidopsis, IGI) - UniProtKB:Q8S8M2 CLE16 (Arabidopsis, IGI) mechanism: IGI PMID:26792519 (TAIR); IMP PMID:26792519 (TAIR); IGI PMID:35519820 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI/IMP row(s) from TAIR on CLE16, CLE17, PP2A3 rest on full text not read here. - go_id: GO:0070382 label: exocytic vesicle aspect: CC annotations: - UniProtKB:F4JQZ3 REN1 (Arabidopsis, IDA) - UniProtKB:Q9LH50 RABA4D (Arabidopsis, IDA) mechanism: IDA PMID:19108776 (TAIR); IDA PMID:18591430 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR on RABA4D, REN1 rest on full text not read here. - go_id: GO:0071318 label: cellular response to ATP aspect: BP annotations: - UniProtKB:Q9LSR8 LECRK19 (Arabidopsis, IMP) mechanism: IMP PMID:24436418 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on LECRK19 rest on full text not read here. - go_id: GO:0043995 label: histone H4K5 acetyltransferase activity aspect: MF annotations: - UniProtKB:Q9FLF7 HAM1 (Arabidopsis, IMP) mechanism: IMP PMID:23273925 (CACAO) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from CACAO on HAM1 rest on full text not read here. - go_id: GO:0030644 label: intracellular chloride ion homeostasis aspect: BP annotations: - UniProtKB:Q9FGT8 TIL (Arabidopsis, IMP) mechanism: IMP PMID:24028869 (UniProt) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from UniProt on TIL rest on full text not read here. - go_id: GO:0098800 label: inner mitochondrial membrane protein complex aspect: CC annotations: - UniProtKB:Q8LAJ9 MIC10 (Arabidopsis, IDA) - UniProtKB:Q9ASV5 MIC60 (Arabidopsis, IDA) mechanism: IDA PMID:26898467 (UniProt); IDA PMID:26898467 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IDA row(s) from TAIR/UniProt on MIC10, MIC60 rest on full text not read here. - go_id: GO:0071475 label: cellular hyperosmotic salinity response aspect: BP annotations: - UniProtKB:F4JUU5 S2P (Arabidopsis, IMP) - UniProtKB:Q9SYK9 UGT74E2 (Arabidopsis, IEP) mechanism: IMP PMID:20876872 (UniProt); IEP PMID:20798329 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IEP/IMP row(s) from TAIR/UniProt on S2P, UGT74E2 rest on full text not read here. - go_id: GO:0098721 label: uracil import across plasma membrane aspect: BP annotations: - UniProtKB:Q3E7D0 NAT12 (Arabidopsis, IBA/IDA) - UniProtKB:Q8GZD4 NAT3 (Arabidopsis, IBA/IDA) mechanism: IBA PANTHER:PTN001671589; IDA PMID:25135661 (TAIR); IBA PANTHER:PTN000122388 verdict: FLAG_FAILS reason: Plant uracil transporters (UPS family) IDA, with IBA seeded by themselves. - go_id: GO:0043144 label: sno(s)RNA processing aspect: BP annotations: - UniProtKB:F4JKB6 PRORP3 (Arabidopsis, IEA/IMP) - UniProtKB:Q680B9 PRORP2 (Arabidopsis, IEA/IMP) mechanism: IEA ARBA:ARBA00084307; IMP PMID:22549728 (TAIR); IMP PMID:22549728 (UniProt) verdict: FLAG_FAILS reason: snoRNA processing IMP and an ARBA IEA on the same proteins; conserved RNA biology. - go_id: GO:0044853 label: plasma membrane raft aspect: CC annotations: - UniProtKB:Q4V3D6 FLOT2 (Arabidopsis, IBA/IDA/IEA) - UniProtKB:Q501E6 FLOT1 (Arabidopsis, IBA/IDA/IEA) - UniProtKB:Q9LV90 FLOT3 (Arabidopsis, IBA/IDA/IEA) mechanism: IBA PANTHER:PTN001013447; IDA PMID:31610051 (TAIR); IEA ARBA:ARBA00026453 verdict: FLAG_FAILS reason: Flotillins are canonical plasma-membrane raft proteins; the IDA, IBA (seeded by AtFLOT loci) and ARBA rows agree. - go_id: GO:0005221 label: intracellularly cyclic nucleotide-activated monoatomic cation channel activity aspect: MF annotations: - UniProtKB:O65718 CNGC2 (Arabidopsis, IMP) mechanism: IMP PMID:10900264 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on CNGC2 rest on full text not read here. - go_id: GO:0019855 label: calcium channel inhibitor activity aspect: MF annotations: - UniProtKB:O22227 MIZ1 (Arabidopsis, IGI) mechanism: IGI PMID:39405435 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IGI row(s) from TAIR on MIZ1 rest on full text not read here. - go_id: GO:0004777 label: succinate-semialdehyde dehydrogenase (NAD+) activity aspect: MF annotations: - UniProtKB:D8QTT0 (Selaginella, IBA/IEA) - UniProtKB:D8RJV5 (Selaginella, IBA/IEA) - UniProtKB:Q9SAK4 ALDH5F1 (Arabidopsis, IBA/IDA/IEA/ISA/ISS) mechanism: IBA PANTHER:PTN008681047; IEA EC:1.2.1.24; IEA UniRule:UR001051784; IEA RHEA:13217; IDA PMID:10517851 (TAIR); ISA from UniProtKB:P51649; ISA from UniProtKB:P51650; ISA from UniProtKB:P76149; ISS from PMID:10517851 verdict: FLAG_FAILS reason: Mitochondrial SSADH (ALDH5F1) of the GABA shunt (IDA); the IBA, EC, RHEA, UniRule and ISA rows agree. - go_id: GO:0050708 label: regulation of protein secretion aspect: BP annotations: - UniProtKB:Q9FK28 MEMB12 (Arabidopsis, IMP) mechanism: IMP PMID:21549312 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on MEMB12 rest on full text not read here. - go_id: GO:0033234 label: negative regulation of protein sumoylation aspect: BP annotations: - UniProtKB:A4GSN8 NUA (Arabidopsis, IMP) mechanism: IMP PMID:17513499 (TAIR) verdict: DEFER_TO_CURATOR reason: The term can apply to plants; IMP row(s) from TAIR on NUA rest on full text not read here. - go_id: GO:0043325 label: phosphatidylinositol-3,4-bisphosphate binding aspect: MF annotations: - UniProtKB:Q8VWF1 SH3P2 (Arabidopsis, IDA) - UniProtKB:Q96262 PCAP1 (Arabidopsis, IDA) mechanism: IDA PMID:28584166 (UniProt); IDA PMID:18397324 (UniProt) verdict: DEFER_TO_CURATOR reason: In vitro lipid binding (IDA) is acceptable as MF, although PI(3,4)P2 is barely detectable in plants; full text not read. - go_id: GO:0043325 label: phosphatidylinositol-3,4-bisphosphate binding aspect: MF annotations: - UniProtKB:D8QYV2 (Selaginella, IBA) mechanism: IBA PANTHER:PTN008555303 verdict: UNCERTAIN reason: PTN008555303 is seeded by TAPP1/TAPP2/DAPP1 and a Dictyostelium protein, so it sits deep. PH-domain phosphoinositide specificity drifts between lineages, and plants lack class I PI3K. Settled by lipid-binding data on the Selaginella protein or an Arabidopsis ortholog. - go_id: GO:0015075 label: monoatomic ion transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q94A76 GORK (Arabidopsis, IMP) mechanism: IMP PMID:24517091 (TAIR) verdict: DEFER_TO_CURATOR reason: GORK is an outward K+ channel; the IMP is correct but general (a K+ channel term fits); the curator can refine. - go_id: GO:0015075 label: monoatomic ion transmembrane transporter activity aspect: MF annotations: - UniProtKB:D8QQK0 (Selaginella, IEA) - UniProtKB:D8R8D0 (Selaginella, IEA) mechanism: IEA InterPro:IPR004686 verdict: UNCERTAIN reason: IPR004686 is the sidoreflexin family, historically called the "tricarboxylate/iron carrier". The characterised members (SFXN1/3) move serine across the mitochondrial inner membrane, so a monoatomic-ion transporter mapping is probably wrong family-wide. Settled by checking the InterPro2GO mapping's provenance. - go_id: GO:0051291 label: protein heterooligomerization aspect: BP annotations: - UniProtKB:Q9FF75 SUN1 (Arabidopsis, IDA/IEA) - UniProtKB:Q9SG79 SUN2 (Arabidopsis, IDA/IEA) mechanism: IDA PMID:19807882 (UniProt); IEA ARBA:ARBA00089325 verdict: FLAG_FAILS reason: SUN1/SUN2 heteromerise (IDA); the ARBA IEA matches. - go_id: GO:0052651 label: monoacylglycerol catabolic process aspect: BP annotations: - UniProtKB:O49523 DSEL (Arabidopsis, IBA/IDA) mechanism: IBA PANTHER:PTN004887113; IDA PMID:21477884 (TAIR) verdict: FLAG_FAILS reason: DSEL lipase IDA on monoacylglycerol, with an IBA seeded by itself; consistent. - go_id: GO:0042246 label: tissue regeneration aspect: BP annotations: - UniProtKB:Q8L5Z1 At1g33811 (Arabidopsis, IEP) - UniProtKB:Q8W485 At5g50100 (Arabidopsis, IMP) mechanism: IEP PMID:35605192 (TAIR); IMP PMID:28724620 (TAIR) verdict: ANNOTATION_WRONG reason: Tissue regeneration is constrained to Metazoa, and GO has plant regeneration terms beside it under GO:0031099. DCC1 (At5g50100) controls shoot regeneration from callus; the GDSL lipase IEP comes from a de novo root regeneration time course. replacement: GO:0062210 shoot regeneration (Q8W485); GO:0062211 root regeneration (Q8L5Z1) supported_by: - reference_id: PMID:28724620 supporting_text: Loss of function of DCC1 resulted in inhibited shoot regeneration. - group: animals_inferred terms: 156 entry_count: 162 verdicts: ANNOTATION_WRONG: 51 FLAG_FAILS: 78 TRUE_BUT_GENERAL: 17 UNCERTAIN: 16 summary: '162 entries over 156 terms: 78 FLAG_FAILS, 51 ANNOTATION_WRONG, 17 TRUE_BUT_GENERAL, 16 UNCERTAIN (no CONSTRAINT_QUESTIONABLE, no DEFER_TO_CURATOR). Wrong rows cluster in five mechanisms: fungal/plant InterPro or ARBA signatures over-matching animal proteins (exomer, UAF, medial cortex, NVJ/Vac8, Inp1 on spartin, plant tetraspanin to auxin, EntA on BDH2, HisKA on a XAB2 fragment); IBA nodes placed above the metazoan branch (Spa2 polarisome on fly piccolo, Swi6/MBF on cec-10, VRG4 GDP-mannose on SLC35D4); rat/RGD source rows whose term misreads the paper, then ISO-propagated to mouse (phenyl acetate esterase read as phenylacetate catabolism, beta-hydroxybutyrate read as poly-hydroxybutyrate, selenite read as selenate, AhR as mating-type transcription, sucrase as beta-fructofuranosidase); old TAS/NAS rows choosing the bacterial isoform of an enzyme class (Si-specific transhydrogenase for NNT, NADH-peroxiredoxin for PRDX3, symmetrical Ap4A hydrolase for NUDT2, Cu(II) pump for ATP7A/B, Kdp-type K+-ATPase for KATP); and homonyms (cytokinin for cytokine on Psg18, ''priming complex'' on YKT6-STX17-SNAP29, host cell plasma membrane on MARCHF8). Most FLAG_FAILS are real but rarely curated animal biology (nematode glyoxylate cycle, Hop2-Mnd1, MOCS3-MOCS2A, curated RHEA side activities) or low-value Ensembl projections of rat IEP rows.' fetched_pmids: [] entries: - go_id: GO:0043332 label: mating projection tip aspect: CC annotations: - UniProtKB:M9PDE7 CG6108 (fly, IBA) mechanism: IBA PANTHER:PTN004550576 (seeds S. cerevisiae SPA2 / S. pombe spa2) verdict: ANNOTATION_WRONG reason: Mating projection tip is a pheromone-induced fungal polarisome structure; a fly piccolo-family protein cannot occupy it. The node carries polarisome CC terms from the yeast Spa2 seeds into the metazoan branch. - go_id: GO:0120105 label: mitotic actomyosin contractile ring, intermediate layer aspect: CC annotations: - UniProtKB:M9PDE7 CG6108 (fly, IBA) mechanism: IBA PANTHER:PTN004550576 (seed S. pombe spa2) verdict: ANNOTATION_WRONG reason: The proximal/intermediate/actin-layer architecture is defined from the fission-yeast ring; a Spa2 seed does not support placing a fly piccolo-family protein in it. Same over-deep node as GO:0043332. - go_id: GO:0044550 label: secondary metabolite biosynthetic process aspect: BP annotations: - UniProtKB:Q95Q02 nrps-1 (worm, IBA) mechanism: IBA PANTHER:PTN002378821 (fungal/bacterial PKS-NRPS seeds) verdict: FLAG_FAILS reason: C. elegans nrps-1 is a hybrid NRPS-PKS gene used with pks-1 to make the nemamide secondary metabolites, so secondary-metabolite biosynthesis applies to this worm protein (from memory of Shou et al. 2016; not re-read). - go_id: GO:0030907 label: MBF transcription complex aspect: CC annotations: - UniProtKB:Q9N4L7 cec-10 (worm, IBA) mechanism: IBA PANTHER:PTN000917496 (Swi6/Cdc10/Res1/Res2 seeds) verdict: ANNOTATION_WRONG reason: MBF requires the fungal KilA-N DNA-binding subunits, which animals lack; consistent with the cec-10 review (REMOVE), which places CEC-10 in the Swi6/Cdc10 subfamily only through ankyrin-region similarity. - go_id: GO:0004038 label: allantoinase activity aspect: MF annotations: - UniProtKB:Q9VWW1 Dmel\CG6106 (fly, IBA) - UniProtKB:Q9VWW1 Dmel\CG6106 (fly, IEA) mechanism: IBA PANTHER:PTN000909483; IEA InterPro IPR017593 (Allantoinase); IEA EC:3.5.2.5 verdict: FLAG_FAILS reason: CG6106 is an allantoinase-family amidohydrolase; insects keep urate oxidase and the ureide pathway that vertebrates lost, so allantoinase is plausible in fly. No direct fly assay was found; a fly enzyme assay would settle it. - go_id: GO:0000256 label: allantoin catabolic process aspect: BP annotations: - UniProtKB:Q8N6M5 ALLC (human, IEA) - UniProtKB:Q9JHX6 Allc (mouse, IEA) mechanism: IEA InterPro IPR005164/IPR015908 (Allantoicase) verdict: ANNOTATION_WRONG reason: Mammals lack allantoicase activity although the ALLC gene is retained, and urate degradation upstream was lost; consistent with the ALLC review (REMOVE). The family-level InterPro2GO mapping should exclude placental mammals. - go_id: GO:0000256 label: allantoin catabolic process aspect: BP annotations: - UniProtKB:Q9VWW1 Dmel\CG6106 (fly, IBA) - UniProtKB:Q9VWW1 Dmel\CG6106 (fly, IEA) mechanism: IBA PANTHER:PTN000909483; IEA InterPro IPR017593; IEA UniPathway UPA00395 verdict: FLAG_FAILS reason: 'Same fly allantoinase as GO:0004038: the ureide pathway is retained in insects, so allantoin catabolism can apply.' - go_id: GO:0004451 label: isocitrate lyase activity aspect: MF annotations: - UniProtKB:Q10663 icl-1 (worm, IBA) - UniProtKB:Q10663 icl-1 (worm, IEA) - UniProtKB:Q10663 icl-1 (worm, ISS) mechanism: IBA PANTHER:PTN000493043; IEA InterPro IPR006254; EC:4.1.3.1; RHEA:13245; ISS verdict: FLAG_FAILS reason: C. elegans ICL-1 is the known bifunctional isocitrate lyase/malate synthase of the nematode glyoxylate cycle; nematodes are a classic animal exception. - go_id: GO:0006097 label: glyoxylate cycle aspect: BP annotations: - UniProtKB:Q10663 icl-1 (worm, IBA) - UniProtKB:Q10663 icl-1 (worm, IEA) - UniProtKB:Q10663 icl-1 (worm, ISS) mechanism: IBA PANTHER:PTN000493043; IEA InterPro IPR019830; UniPathway UPA00703; ISS verdict: FLAG_FAILS reason: Nematodes run a glyoxylate cycle through ICL-1; the GO constraint only excludes Deuterostomia, so the worm row is consistent with it. - go_id: GO:0017102 label: methionyl glutamyl tRNA synthetase complex aspect: CC annotations: - UniProtKB:Q23315 ears-1 (worm, IBA) mechanism: IBA PANTHER:PTN000012559 (yeast GUS1, pombe gus1 seeds) verdict: UNCERTAIN reason: The term is modelled on the yeast Arc1-MetRS-GluRS complex; in animals GluRS and MetRS sit in the larger multi-synthetase complex (GO:0017101). Whether worm EARS-1 associates with MetRS (and so meets the bare definition) needs a nematode complex study. - go_id: GO:0000171 label: ribonuclease MRP activity aspect: MF annotations: - UniProtKB:O75818 RPP40 (human, IBA) - UniProtKB:Q8R1F9 Rpp40 (mouse, IBA) - UniProtKB:Q9DB28 Pop5 (mouse, ISA) mechanism: IBA PANTHER:PTN001034909; ISA from yeast POP5 verdict: FLAG_FAILS reason: RNase MRP exists in animals (RMRP RNA) and RPP40 and POP5 are shared protein subunits of human RNase P and MRP. - go_id: GO:0016854 label: racemase and epimerase activity aspect: MF annotations: - UniProtKB:Q17993 rml-3 (worm, IBA) mechanism: IBA PANTHER:PTN000471580 (RmlC seeds) verdict: TRUE_BUT_GENERAL reason: C. elegans has a dTDP-rhamnose pathway (rml genes) and rml-3 is the RmlC epimerase; the specific activity term fits. replacement: GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity - go_id: GO:0016854 label: racemase and epimerase activity aspect: MF annotations: - UniProtKB:Q9BPW9 DHRS9 (human, NAS) mechanism: NAS PMID:11294878 (UniProt) verdict: UNCERTAIN reason: DHRS9 curated function (UniProt) is 3-alpha-HSD and retinol dehydrogenase, with no epimerase statement; reading PMID:11294878 for a 3alpha-to-3beta epimerase claim would settle it. - go_id: GO:0000709 label: meiotic joint molecule formation aspect: BP annotations: - UniProtKB:A0A8V0ZJB7 PSMC3IP (chicken, IBA) - UniProtKB:O35047 Psmc3ip (mouse, IBA) - UniProtKB:Q9P2W1 PSMC3IP (human, IBA) mechanism: IBA PANTHER:PTN000409077 (seed pombe meu13/Hop2) verdict: FLAG_FAILS reason: Hop2-Mnd1 (PSMC3IP) promotes DMC1/RAD51 strand invasion and joint-molecule formation in mammalian meiosis. - go_id: GO:0010774 label: meiotic strand invasion involved in reciprocal meiotic recombination aspect: BP annotations: - UniProtKB:A0A8V0ZJB7 PSMC3IP (chicken, IBA) - UniProtKB:O35047 Psmc3ip (mouse, IBA) - UniProtKB:Q9P2W1 PSMC3IP (human, IBA) mechanism: IBA PANTHER:PTN000409077 verdict: FLAG_FAILS reason: Mouse Hop2 is required for meiotic strand invasion; same node as GO:0000709. - go_id: GO:0120231 label: DNA recombinase auxiliary factor complex aspect: CC annotations: - UniProtKB:A0A8V0ZJB7 PSMC3IP (chicken, IBA) - UniProtKB:O35047 Psmc3ip (mouse, IBA) - UniProtKB:Q9P2W1 PSMC3IP (human, IBA) mechanism: IBA PANTHER:PTN000409077 verdict: FLAG_FAILS reason: Hop2-Mnd1 is the mammalian recombinase auxiliary complex; same node as GO:0000709. - go_id: GO:0016156 label: fumarate reductase (NADH) activity aspect: MF annotations: - UniProtKB:Q09567 (worm, IBA) - UniProtKB:Q09567 (worm, IEA) mechanism: IBA PANTHER:PTN005162385 (yeast FRD1/OSM1, T. brucei seeds); IEA EC:1.3.1.6 verdict: FLAG_FAILS reason: F48E8.3 is a soluble FRD1/OSM1-family fumarate reductase (protein-level existence); invertebrates retain this family, and nothing shows the worm protein lost the activity. - go_id: GO:1990133 label: molybdopterin adenylyltransferase complex aspect: CC annotations: - UniProtKB:P0C919 Mocs2A (fly, IBA) - UniProtKB:P0C919 Mocs2A (fly, ISS) - UniProtKB:Q09412 moc-6 (worm, IBA) - UniProtKB:Q9VLJ8 Mocs3 (fly, ISS) mechanism: IBA PANTHER:PTN008655638; ISS from E. coli MoaD/MoeB verdict: FLAG_FAILS reason: The term definition names human MOCS3-MOCS2A as the eukaryotic complex; fly and worm orthologues fit. - go_id: GO:0009787 label: regulation of abscisic acid-activated signaling pathway aspect: BP annotations: - UniProtKB:A0A8V0XMZ9 LANCL2 (chicken, IBA) - UniProtKB:Q9JJK2 Lancl2 (mouse, IBA) - UniProtKB:Q9NS86 LANCL2 (human, IBA) mechanism: IBA PANTHER:PTN000296773 (seeds Arabidopsis GCR2/AT1G52920, human LANCL2) verdict: UNCERTAIN reason: The plant seed GCR2 was proposed as an ABA receptor and later disputed; mammalian LANCL2-ABA signalling comes mainly from one group. An independent replication of ABA binding/signalling by LANCL2 would settle whether this BP should exist in vertebrates. - go_id: GO:0015112 label: nitrate transmembrane transporter activity aspect: MF annotations: - UniProtKB:A0A2R8VHB9 Aqp6 (mouse, ISO) - UniProtKB:Q13520 AQP6 (human, IBA) - UniProtKB:Q8C4A0 Aqp6 (mouse, IBA) - UniProtKB:Q8C4A0 Aqp6 (mouse, ISO) mechanism: IBA PANTHER:PTN001452348; ISO from rat Aqp6 (IMP PMID:12177001) verdict: FLAG_FAILS reason: AQP6 is an anion channel permeable to nitrate (rat IMP source), so the activity applies. - go_id: GO:0000719 label: photoreactive repair aspect: BP annotations: - UniProtKB:A0A8V0YRT6 LOC424919 (chicken, IBA) mechanism: IBA PANTHER:PTN000025285 (seed Arabidopsis PHR1) verdict: FLAG_FAILS reason: The chicken protein is a class II CPD photolyase (UniProt family); non-placental vertebrates retain photoreactivation, which placental mammals lost. A chicken activity assay would confirm. - go_id: GO:0005458 label: GDP-mannose transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q24JQ0 SLC35D4 (human, IBA) - UniProtKB:Q3UME2 Slc35d4 (mouse, IBA) mechanism: IBA PANTHER:PTN000744836 (seeds yeast VRG4, Arabidopsis GONST1) verdict: ANNOTATION_WRONG reason: SLC35D4 is a Golgi UDP-GlcNAc transporter (UniProt FUNCTION, PubMed:37890669); mammals have no Golgi GDP-mannose transporter. The node is placed above the SLC35D4 branch. - go_id: GO:1990570 label: GDP-mannose transmembrane transport aspect: BP annotations: - UniProtKB:Q24JQ0 SLC35D4 (human, IBA) - UniProtKB:Q3UME2 Slc35d4 (mouse, IBA) mechanism: IBA PANTHER:PTN000744836 verdict: ANNOTATION_WRONG reason: Same over-deep node as GO:0005458; SLC35D4 transports UDP-GlcNAc, not GDP-mannose. - go_id: GO:0032135 label: DNA insertion or deletion binding aspect: MF annotations: - UniProtKB:A0A8V0XSB3 MSH3 (chicken, IBA) - UniProtKB:P13705 Msh3 (mouse, IBA) - UniProtKB:P20585 MSH3 (human, IBA) mechanism: IBA PANTHER:PTN000145759 verdict: FLAG_FAILS reason: MutSbeta (MSH2-MSH3) recognises insertion/deletion loops in mammals. - go_id: GO:0008663 label: 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity aspect: MF annotations: - UniProtKB:A0A8V1AKT7 ADPRM (chicken, IBA) - UniProtKB:Q3LIE5 ADPRM (human, IBA) - UniProtKB:Q99KS6 Adprm (mouse, IBA) mechanism: IBA PANTHER:PTN000421113 (seed zebrafish adprm) verdict: UNCERTAIN reason: Human ADPRM substrate panel (UniProt FUNCTION, PubMed:25692488) lists ADP-ribose, CDP-alcohols and cADPR but not 2',3'-cyclic nucleotides; the zebrafish source paper and a human assay on 2',3'-cAMP would settle it. - go_id: GO:0035485 label: adenine/guanine mispair binding aspect: MF annotations: - UniProtKB:A0A8V1AAE7 MUTYH (chicken, IBA) - UniProtKB:Q99P21 Mutyh (mouse, IBA) - UniProtKB:Q9UIF7 MUTYH (human, IBA) mechanism: IBA PANTHER:PTN000040628 verdict: FLAG_FAILS reason: MUTYH binds A:G and A:8-oxoG mispairs in mammals. - go_id: GO:0097505 label: Rad6-Rad18 complex aspect: CC annotations: - UniProtKB:A0A8V0Z470 RAD18 (chicken, IBA) - UniProtKB:Q9NS91 RAD18 (human, IBA) - UniProtKB:Q9QXK2 Rad18 (mouse, IBA) mechanism: IBA PANTHER:PTN001020335 verdict: FLAG_FAILS reason: RAD6-RAD18 complex is well established in human cells; consistent with the RAD18 review (ACCEPT). - go_id: GO:0000481 label: maturation of 5S rRNA aspect: BP annotations: - UniProtKB:O01524 snu-66 (worm, IBA) - UniProtKB:O43290 SART1 (human, IBA) - UniProtKB:Q9Z315 Sart1 (mouse, IBA) mechanism: IBA PANTHER:PTN000365724 (seed yeast SNU66; IMP/IGI PMID:19806183) verdict: UNCERTAIN reason: The node propagates a single yeast genetic-network result for the tri-snRNP protein Snu66 to all SART1 orthologues; no metazoan evidence links SART1 to 5S rRNA processing. A metazoan 5S rRNA assay after SART1 depletion would settle it. - go_id: GO:0000160 label: phosphorelay signal transduction system aspect: BP annotations: - UniProtKB:F6TM12 Xab2 (mouse, IEA) mechanism: IEA GOC inference from GO:0000155 (itself IEA InterPro IPR003661) verdict: ANNOTATION_WRONG reason: Derived from the bad GO:0000155 row on the same Xab2 fragment; XAB2 is a HAT-repeat spliceosome protein, not a two-component kinase. - go_id: GO:0000155 label: phosphorelay sensor kinase activity aspect: MF annotations: - UniProtKB:F6TM12 Xab2 (mouse, IEA) mechanism: IEA InterPro IPR003661 (HisKA dimerisation/phosphoacceptor domain) verdict: ANNOTATION_WRONG reason: F6TM12 is a 285-aa TrEMBL fragment of the splicing factor XAB2; a lone HisKA signature hit on it cannot make it a phosphorelay sensor kinase, which animals do not have. - go_id: GO:0016625 label: oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor aspect: MF annotations: - UniProtKB:A0A494BB43 Sting1 (mouse, IEA) mechanism: IEA InterPro IPR036021 (aldehyde ferredoxin oxidoreductase-like C-terminal superfamily) verdict: ANNOTATION_WRONG reason: A spurious superfamily hit on a 204-aa STING1 TrEMBL entry; STING has no iron-sulfur oxidoreductase activity and animals lack AOR-type enzymes. - go_id: GO:0031097 label: medial cortex aspect: CC annotations: - UniProtKB:Q9VZ85 RhoGEF64C (fly, IEA) mechanism: IEA ARBA:ARBA00049834 verdict: ANNOTATION_WRONG reason: Medial cortex is the fission-yeast nuclear-positioned cortical band that sets the ring position; it does not exist as such in fly cells. - go_id: GO:0009734 label: auxin-activated signaling pathway aspect: BP annotations: - UniProtKB:A0ACI8SBU2 TSPAN13 (human, IEA) mechanism: IEA InterPro IPR044991 (Tetraspanin, plant) verdict: ANNOTATION_WRONG reason: Auxin signalling is plant-specific; the plant-tetraspanin family signature over-matches human TSPAN13 and its InterPro2GO mapping should not reach animals. - go_id: GO:0140098 label: catalytic activity, acting on RNA aspect: MF annotations: - UniProtKB:E1JJR3 pcm (fly, IEA) - UniProtKB:Q9VWI1 pcm (fly, IEA) mechanism: IEA ARBA:ARBA00027979 verdict: TRUE_BUT_GENERAL reason: Pacman is XRN1, a 5'-3' exoribonuclease. replacement: GO:0004534 5'-3' RNA exonuclease activity - go_id: GO:0000500 label: RNA polymerase I upstream activating factor complex aspect: CC annotations: - UniProtKB:Q22749 (worm, IEA) mechanism: IEA ARBA:ARBA00091673 verdict: ANNOTATION_WRONG reason: UAF (Rrn5/Rrn9/Rrn10/Uaf30) is a yeast-specific Pol I factor; a worm DM2/SWIB-domain protein shares only the Uaf30 domain. - go_id: GO:0034044 label: exomer complex aspect: CC annotations: - UniProtKB:H0Y6S0 TTC17 (human, IEA) mechanism: IEA ARBA:ARBA00028457 verdict: ANNOTATION_WRONG reason: Exomer (Chs5-ChAPs) is a fungal TGN cargo adaptor absent from animals; TTC17 shares TPR repeats only. - go_id: GO:0045033 label: peroxisome inheritance aspect: BP annotations: - UniProtKB:O44735 spg-20 (worm, IEA) mechanism: IEA InterPro IPR024758 (Inheritance of peroxisomes protein 1) verdict: ANNOTATION_WRONG reason: Worm SPG-20 is the spartin orthologue (MIT plus senescence domain); the Inp1 family signature over-matches it, and yeast Inp1-mediated peroxisome retention has no shown metazoan counterpart. - go_id: GO:0005780 label: extrinsic component of intraperoxisomal membrane aspect: CC annotations: - UniProtKB:O44735 spg-20 (worm, IEA) mechanism: IEA InterPro IPR024758 verdict: ANNOTATION_WRONG reason: Same Inp1 over-match on spartin as GO:0045033. - go_id: GO:0120029 label: proton export across plasma membrane aspect: BP annotations: - UniProtKB:Q21461 (worm, IEA) mechanism: IEA InterPro IPR004712 (Na+/H+ antiporter, fungi) verdict: UNCERTAIN reason: M02D8.3 is uncharacterised; fungal Nha1-type antiporters normally extrude Na+/K+ in exchange for H+ entry, so a proton-export mapping for this family is itself doubtful. The InterPro2GO rationale and a worm transport assay would settle it. - go_id: GO:0045017 label: glycerolipid biosynthetic process aspect: BP annotations: - UniProtKB:Q9VJ41 Dmel\CG33120 (fly, IEA) mechanism: IEA InterPro IPR045034 (WSD1-like O-acyltransferase) verdict: UNCERTAIN reason: Glycerolipid synthesis is ubiquitous in animals, but whether fly CG33120 has the WS/DGAT acyltransferase activity of the bacterial/plant family is untested; an acyltransferase assay would settle it. - go_id: GO:0031408 label: oxylipin biosynthetic process aspect: BP annotations: - UniProtKB:Q02928 CYP4A11 (human, IEA) - UniProtKB:Q9HBI6 CYP4F11 (human, IEA) mechanism: IEA UniPathway UPA00382 verdict: TRUE_BUT_GENERAL reason: The definition is generic (oxidative PUFA metabolites); CYP4A11/CYP4F11 make 20-HETE and other hydroxy-eicosanoids, so icosanoid synthesis is the precise process. replacement: GO:0046456 icosanoid biosynthetic process - go_id: GO:0045936 label: negative regulation of phosphate metabolic process aspect: BP annotations: - UniProtKB:A0A8V0XX26 EPM2A (chicken, IEA) - UniProtKB:O95278 EPM2A (human, IEA) - UniProtKB:Q9WUA5 Epm2a (mouse, IEA) mechanism: IEA ARBA:ARBA00028171 verdict: UNCERTAIN reason: 'Consistent with the EPM2A review (UNDECIDED): the ARBA rule cites no experiment for negative regulation, and laforin''s glucan dephosphorylation is itself phosphate metabolism rather than regulation of it.' - go_id: GO:0009693 label: ethylene biosynthetic process aspect: BP annotations: - UniProtKB:A0A8V0XID9 ACCSL (chicken, IEA) mechanism: IEA ARBA:ARBA00091972 verdict: ANNOTATION_WRONG reason: Animals do not make ethylene; ACCSL keeps the ACC-synthase fold only by descent. - go_id: GO:0009863 label: salicylic acid mediated signaling pathway aspect: BP annotations: - UniProtKB:Q9VR90 Syx16 (fly, IEA) mechanism: IEA ARBA:ARBA00084971 verdict: ANNOTATION_WRONG reason: Salicylic-acid signalling is a plant hormone pathway; a fly syntaxin cannot participate. - go_id: GO:0072521 label: purine-containing compound metabolic process aspect: BP annotations: - UniProtKB:A0A8V0YG94 GARTL (chicken, IEA) - UniProtKB:A0ACP0M6V1 Gart (mouse, IEA) - UniProtKB:Q20143 (worm, IEA) mechanism: IEA ARBA:ARBA00026860 verdict: TRUE_BUT_GENERAL reason: GART is the trifunctional de novo purine enzyme. replacement: GO:0006189 'de novo' IMP biosynthetic process - go_id: GO:0000393 label: spliceosomal conformational changes to generate catalytic conformation aspect: BP annotations: - UniProtKB:P34369 prp-8 (worm, IEA) - UniProtKB:Q9U2G0 snrp-200 (worm, IEA) mechanism: IEA ARBA:ARBA00089929 verdict: FLAG_FAILS reason: Prp8 and Brr2 drive catalytic activation of the spliceosome in all eukaryotes. - go_id: GO:0061804 label: mitotic spindle formation (spindle phase one) aspect: BP annotations: - UniProtKB:G5ECF4 bmk-1 (worm, IEA) - UniProtKB:G5EGL7 bmk-1 (worm, IEA) mechanism: IEA ARBA:ARBA00090575 verdict: FLAG_FAILS reason: The definition is generic (pole separation in prophase) and kinesin-5 BMK-1 separates poles in animals. - go_id: GO:0015556 label: C4-dicarboxylate transmembrane transporter activity aspect: MF annotations: - UniProtKB:E1JIQ7 CG32921-ORFB (fly, IEA) - UniProtKB:Q0KI47 anon-WO0140519.217 (fly, IEA) - UniProtKB:Q7KTF1 Dmel\CG7309 (fly, IEA) mechanism: IEA ARBA:ARBA00033521 verdict: FLAG_FAILS reason: Indy is an SLC13 transporter of citrate and other C4-dicarboxylate Krebs intermediates. - go_id: GO:0008667 label: 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity aspect: MF annotations: - UniProtKB:D6R9U8 BDH2 (human, IEA) mechanism: IEA InterPro IPR003560 (EntA family) verdict: ANNOTATION_WRONG reason: BDH2 is a 4-oxo-L-proline reductase/3-hydroxybutyrate dehydrogenase (UniProt FUNCTION, PubMed:35150746); animals lack the isochorismate route that produces the 2,3-dihydrodiol substrate. The EntA family signature over-matches the SDR fold. - go_id: GO:0071562 label: nucleus-vacuole junction assembly aspect: BP annotations: - UniProtKB:A0A8V0XKW8 LOC421690 (chicken, IEA) - UniProtKB:A0A8V0XTI8 LOC421690 (chicken, IEA) mechanism: IEA InterPro IPR045156 (Vacuolar protein 8) verdict: ANNOTATION_WRONG reason: The nucleus-vacuole junction (Nvj1-Vac8) is a yeast structure; the Vac8 family signature over-matches a chicken ARM-repeat protein. - go_id: GO:0043436 label: oxoacid metabolic process aspect: BP annotations: - UniProtKB:P20478 Gs2 (fly, IEA) - UniProtKB:X2JDA5 Gs2 (fly, IEA) mechanism: IEA ARBA:ARBA00027279 verdict: TRUE_BUT_GENERAL reason: Gs2 is glutamine synthetase. replacement: GO:1901704 L-glutamine biosynthetic process - go_id: GO:0015980 label: energy derivation by oxidation of organic compounds aspect: BP annotations: - UniProtKB:A0ACI8UJF7 PDHA1 (human, IEA) mechanism: IEA ARBA:ARBA00026991 verdict: TRUE_BUT_GENERAL reason: PDHA1 is the E1 alpha subunit of pyruvate dehydrogenase. replacement: GO:0006086 pyruvate decarboxylation to acetyl-CoA - go_id: GO:0015980 label: energy derivation by oxidation of organic compounds aspect: BP annotations: - UniProtKB:P49748 ACADVL (human, TAS) mechanism: TAS PMID:7479827 verdict: FLAG_FAILS reason: Consistent with the ACADVL review (KEEP_AS_NON_CORE); energy derivation from fatty acids is animal biology. - go_id: GO:0015980 label: energy derivation by oxidation of organic compounds aspect: BP annotations: - UniProtKB:Q08AH1 ACSM1 (human, NAS) mechanism: NAS PMID:11470804 verdict: TRUE_BUT_GENERAL reason: PMID:11470804 shows ACSM1 (MACS1) acyl-CoAs are used mainly for oxidation; the precise process is fatty acid beta-oxidation. replacement: GO:0006635 fatty acid beta-oxidation - go_id: GO:0140085 label: L-amino-acid N-acetyltransferase activity aspect: MF annotations: - UniProtKB:A0ACP2IEB2 NAGS (human, IEA) mechanism: IEA ARBA:ARBA00084890 verdict: TRUE_BUT_GENERAL reason: NAGS acetylates L-glutamate. replacement: GO:0004042 L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donor - go_id: GO:0016781 label: phosphotransferase activity, paired acceptors aspect: MF annotations: - UniProtKB:Q22649 (worm, IEA) mechanism: IEA ARBA:ARBA00087648 verdict: FLAG_FAILS reason: Q22649 carries PEP-utilising/PPDK domains, and the paired-acceptor class correctly covers either PEP synthase or PPDK; a worm assay would say which. - go_id: GO:0016782 label: transferase activity, transferring sulphur-containing groups aspect: MF annotations: - UniProtKB:Q19434 scly-1 (worm, IEA) mechanism: IEA ARBA:ARBA00026283 verdict: ANNOTATION_WRONG reason: SCLY-1 is selenocysteine lyase (EC 4.4.1.16), a lyase, not a sulphur-group transferase. replacement: GO:0009000 selenocysteine lyase activity - go_id: GO:0005527 label: macrolide binding aspect: MF annotations: - UniProtKB:P54397 Fkbp39 (fly, IEA) - UniProtKB:P62942 FKBP1A (human, NAS) mechanism: IEA ARBA:ARBA00086867; NAS PMID:17962721 verdict: TRUE_BUT_GENERAL reason: FKBPs bind the macrolides FK506 and rapamycin. replacement: GO:0005528 FK506 binding - go_id: GO:1903844 label: regulation of cellular response to transforming growth factor beta stimulus aspect: BP annotations: - UniProtKB:Q9W1N4 wmd (fly, IEA) mechanism: IEA ARBA:ARBA00033909 verdict: FLAG_FAILS reason: STRAP (wmd) is a TGF-beta receptor-associated regulator; the TGF-beta pathway is animal biology. - go_id: GO:0031559 label: oxidosqualene cyclase activity aspect: MF annotations: - UniProtKB:A0A0G2JQD0 LSS (human, IEA) - UniProtKB:A0A8V0YEB4 LSS (chicken, IEA) - UniProtKB:A0ACI8S916 LSS (human, IEA) mechanism: IEA ARBA:ARBA00026617 verdict: TRUE_BUT_GENERAL reason: LSS is lanosterol synthase. replacement: GO:0000250 lanosterol synthase activity - go_id: GO:0045937 label: positive regulation of phosphate metabolic process aspect: BP annotations: - UniProtKB:A0ACI8R7Y5 SRC (human, IEA) - UniProtKB:P12931 SRC (human, IEA) mechanism: IEA ARBA:ARBA00028182 verdict: TRUE_BUT_GENERAL reason: 'Consistent with the SRC review (MARK_AS_OVER_ANNOTATED): true but too vague to add anything beyond its tyrosine kinase activity.' - go_id: GO:0000992 label: RNA polymerase III cis-regulatory region sequence-specific DNA binding aspect: MF annotations: - UniProtKB:P20227 Tbp (fly, IEA) - UniProtKB:Q27896 Trf (fly, IEA) mechanism: IEA ARBA:ARBA00092969 verdict: FLAG_FAILS reason: TBP binds Pol III promoters and fly TRF1 is a Pol III factor. - go_id: GO:0052716 label: hydroquinone:oxygen oxidoreductase activity aspect: MF annotations: - UniProtKB:A1Z6F5 stw (fly, IEA) mechanism: IEA EC:1.10.3.2 verdict: FLAG_FAILS reason: Fly Laccase 2 is the cuticle-tanning laccase. - go_id: GO:0080146 label: L-cysteine desulfhydrase activity aspect: MF annotations: - UniProtKB:P32929 CTH (human, IEA) - UniProtKB:Q8VCN5 Cth (mouse, IEA) mechanism: IEA RHEA:24931 verdict: FLAG_FAILS reason: 'Consistent with the CTH review (KEEP_AS_NON_CORE): a curated secondary activity.' - go_id: GO:0045551 label: cinnamyl-alcohol dehydrogenase activity aspect: MF annotations: - UniProtKB:O60218 AKR1B10 (human, IEA) mechanism: IEA RHEA:10392 verdict: FLAG_FAILS reason: UniProt records the cinnamaldehyde reduction with experimental evidence (PubMed:36966166); a broad-substrate AKR activity. - go_id: GO:0032866 label: D-xylose reductase (NADPH) activity aspect: MF annotations: - UniProtKB:P15121 AKR1B1 (human, IEA) - UniProtKB:P45376 Akr1b1 (mouse, IEA) mechanism: IEA RHEA:27445 verdict: FLAG_FAILS reason: D-xylose is a classic aldose-reductase substrate (UniProt, PubMed:1936586, 4402695). - go_id: GO:0032867 label: L-arabinose reductase (NADPH) activity aspect: MF annotations: - UniProtKB:P15121 AKR1B1 (human, IEA) - UniProtKB:P45376 Akr1b1 (mouse, IEA) mechanism: IEA RHEA:25229 verdict: FLAG_FAILS reason: L-arabinose reduction by AKR1B1 is curated with experimental evidence (PubMed:4402695). - go_id: GO:0016906 label: sterol 3-beta-glucosyltransferase activity aspect: MF annotations: - UniProtKB:P16662 UGT2B7 (human, IEA) mechanism: IEA RHEA:22724 verdict: FLAG_FAILS reason: UniProt curates UGT2B7 sterol glucosylation with experimental evidence (PubMed:9169006); in-vitro breadth of a UGT. - go_id: GO:0140401 label: 4-phosphoerythronate phosphatase activity aspect: MF annotations: - UniProtKB:A6NDG6 PGP (human, IEA) - UniProtKB:Q5F4B1 PGP (chicken, IEA) - UniProtKB:Q8CHP8 Pgp (mouse, IEA) mechanism: IEA RHEA:86555 verdict: FLAG_FAILS reason: PGP removes 4-phosphoerythronate in mammals (UniProt, PubMed:27294321). - go_id: GO:0106009 label: (4S)-4-hydroxy-2-oxoglutarate aldolase activity aspect: MF annotations: - UniProtKB:Q86XE5 HOGA1 (human, IEA) - UniProtKB:Q9DCU9 Hoga1 (mouse, IEA) mechanism: IEA RHEA:35639 verdict: FLAG_FAILS reason: Consistent with the HOGA1 review (ACCEPT). - go_id: GO:0004071 label: aspartate-ammonia ligase activity aspect: MF annotations: - UniProtKB:P08243 ASNS (human, IEA) - UniProtKB:Q5ZJU3 ASNS (chicken, IEA) - UniProtKB:Q61024 Asns (mouse, IEA) mechanism: IEA RHEA:11372 verdict: FLAG_FAILS reason: 'Consistent with the ASNS review (KEEP_AS_NON_CORE): measured ammonia-fed mode.' - go_id: GO:0016041 label: glutamate synthase (ferredoxin) activity aspect: MF annotations: - UniProtKB:M9PCU8 Glts (fly, IEA) mechanism: IEA EC:1.4.7.1 (UniProt name) verdict: ANNOTATION_WRONG reason: Ferredoxin-dependent GOGAT is a plant/cyanobacterial enzyme; animal GOGAT is the NADH-dependent type. The EC was assigned automatically to the fly entry name. replacement: GO:0016040 glutamate synthase (NADH) activity - go_id: GO:0008783 label: agmatinase activity aspect: MF annotations: - UniProtKB:Q90XD2 AGMAT (chicken, IEA) - UniProtKB:Q90XD2 AGMAT (chicken, ISS) - UniProtKB:Q9BSE5 AGMAT (human, TAS) mechanism: IEA EC:3.5.3.11; IEA RHEA:13929; ISS from human; TAS Reactome R-HSA-350604 verdict: ANNOTATION_WRONG reason: Human AGMAT is a guanidino-acid hydrolase that is virtually inactive with agmatine; the chicken rows inherit the human claim via ISS and the old EC name. supported_by: - reference_id: PMID:36543883 supporting_text: Here we show that AGMAT hydrolyzed a range of linear guanidino acids but was virtually inactive with agmatine. - go_id: GO:0008881 label: glutamate racemase activity aspect: MF annotations: - UniProtKB:D3Z0F6 Sdsl (mouse, ISO) - UniProtKB:Q8R238 Sdsl (mouse, IEA) - UniProtKB:Q8R238 Sdsl (mouse, ISO) - UniProtKB:Q8R238 Sdsl (mouse, ISS) - UniProtKB:Q96GA7 SDSL (human, IEA) - UniProtKB:Q96GA7 SDSL (human, ISS) mechanism: ISO from rat Sdsl (IDA PMID:33079132); ISS; IEA EC/RHEA verdict: FLAG_FAILS reason: Rat SDSL has measured glutamate racemase activity (PMID:33079132) and D-glutamate exists in mammals. - go_id: GO:0009751 label: response to salicylic acid aspect: BP annotations: - UniProtKB:P58743 SLC26A5 (human, IEA) - UniProtKB:Q64471 Gstt1 (mouse, IEA) - UniProtKB:Q99NH7 Slc26a5 (mouse, IEA) mechanism: IEA Ensembl projection of rat IEP (PMID:19173110, PMID:9729437) verdict: FLAG_FAILS reason: Response to salicylate is chemically possible in animals (prestin is a classic salicylate target); the rows are low-value projections of rat expression-pattern data, not a lineage error. - go_id: GO:0009645 label: response to low light intensity stimulus aspect: BP annotations: - UniProtKB:P15499 Prph2 (mouse, IEA) - UniProtKB:P23942 PRPH2 (human, IEA) mechanism: IEA Ensembl projection of rat IEP (PMID:8320859) verdict: FLAG_FAILS reason: Retinal responses to dim light are animal biology; a projected rat IEP row of low value. - go_id: GO:2001040 label: positive regulation of cellular response to drug aspect: BP annotations: - UniProtKB:Q9UMX1 SUFU (human, IEA) - UniProtKB:Q9Z0P7 Sufu (mouse, IEA) mechanism: IEA Ensembl projection of rat IEP (PMID:30790292) verdict: ANNOTATION_WRONG reason: 'Consistent with the SUFU review (REMOVE): a glioma-cell drug-sensitivity observation propagated as a process.' - go_id: GO:1905534 label: positive regulation of L-leucine import across plasma membrane aspect: BP annotations: - UniProtKB:Q01650 SLC7A5 (human, IEA) - UniProtKB:Q9Z127 Slc7a5 (mouse, IEA) - UniProtKB:Q9Z127 Slc7a5 (mouse, ISO) mechanism: IEA Ensembl projection + ISO from rat Slc7a5 (IMP PMID:25049270) verdict: UNCERTAIN reason: SLC7A5 is itself the leucine importer, so "positive regulation of import" may be a sense error for GO:1903801-type import; reading PMID:25049270 would settle it. - go_id: GO:0048313 label: Golgi inheritance aspect: BP annotations: - UniProtKB:P31938 Map2k1 (mouse, IEA) - UniProtKB:P31938 Map2k1 (mouse, ISO) - UniProtKB:P53350 PLK1 (human, TAS) - UniProtKB:Q02750 MAP2K1 (human, IEA) mechanism: IEA Ensembl projection; ISO from rat Map2k1; TAS Reactome verdict: FLAG_FAILS reason: 'Consistent with the PLK1 and MAP2K1 reviews (KEEP_AS_NON_CORE): mitotic Golgi partitioning is animal biology.' - go_id: GO:0060359 label: response to ammonium ion aspect: BP annotations: - UniProtKB:P30520 ADSS2 (human, IEA) - UniProtKB:P46664 Adss2 (mouse, IEA) mechanism: IEA Ensembl projection of rat IEP (PMID:6838904) verdict: FLAG_FAILS reason: Hyperammonaemia responses are animal biology; low-value IEP projection. - go_id: GO:0070676 label: intralumenal vesicle formation aspect: BP annotations: - UniProtKB:A0A8V1AHN5 RILP (chicken, IEA) - UniProtKB:Q5ND29 Rilp (mouse, IEA) mechanism: IEA Ensembl projection from human RILP verdict: FLAG_FAILS reason: RILP recruits ESCRT-II to endosomes in mammals. - go_id: GO:2000784 label: positive regulation of establishment of cell polarity regulating cell shape aspect: BP annotations: - UniProtKB:A0A494B9A7 Cfl1 (mouse, ISO) - UniProtKB:P18760 Cfl1 (mouse, IEA) - UniProtKB:P18760 Cfl1 (mouse, ISO) - UniProtKB:P23528 CFL1 (human, IEA) mechanism: IEA Ensembl projection; ISO from rat Cfl1 (IMP PMID:26169356) verdict: FLAG_FAILS reason: Cofilin-driven polarity and cell shape is animal biology. - go_id: GO:0048571 label: long-day photoperiodism aspect: BP annotations: - UniProtKB:O00253 AGRP (human, IEA) - UniProtKB:P56473 Agrp (mouse, IEA) mechanism: IEA Ensembl projection of rat IEP (PMID:19490367) verdict: FLAG_FAILS reason: Photoperiodism exists in seasonal mammals; low-value IEP projection. - go_id: GO:0016679 label: oxidoreductase activity, acting on diphenols and related substances as donors aspect: MF annotations: - UniProtKB:P00184 Cyp1a1 (mouse, IEA) - UniProtKB:P00184 Cyp1a1 (mouse, ISO) - UniProtKB:P04798 CYP1A1 (human, IEA) mechanism: IEA Ensembl projection; ISO from rat Cyp1a1 (IDA PMID:12054491) verdict: ANNOTATION_WRONG reason: 'Consistent with the Cyp1a1 review (REMOVE): chemically mismatched for a P450 monooxygenase.' - go_id: GO:0010124 label: phenylacetate catabolic process aspect: BP annotations: - UniProtKB:D6RJ12 Pon3 (mouse, ISO) - UniProtKB:H3BL07 Pon3 (mouse, ISO) - UniProtKB:Q62087 Pon3 (mouse, ISO) mechanism: ISO from rat Pon3 (IDA PMID:12946270) verdict: ANNOTATION_WRONG reason: The rat paper purified PON3 and assayed esterase activity; phenyl acetate (an ester substrate) appears to have been read as phenylacetate catabolism. The MF behind it is arylesterase activity. replacement: GO:0004064 arylesterase activity (MF) - go_id: GO:0033797 label: selenate reductase activity aspect: MF annotations: - UniProtKB:A0A1W2P6U1 Txnrd1 (mouse, ISO) - UniProtKB:Q9JMH6 Txnrd1 (mouse, ISO) mechanism: ISO from rat Txnrd1 (IDA PMID:20810785) verdict: ANNOTATION_WRONG reason: The source paper concerns selenite rescue of mercury-inhibited TrxR, not selenate reduction; selenate reductase is a bacterial molybdoenzyme activity. - go_id: GO:0031405 label: lipoic acid binding aspect: MF annotations: - UniProtKB:A0A140LI30 Insr (mouse, ISO) - UniProtKB:A0A140LIH1 Insr (mouse, ISO) - UniProtKB:P15208 Insr (mouse, ISO) mechanism: ISO from rat Insr (IPI PMID:17274632) verdict: UNCERTAIN reason: The rat source rests on computer docking plus kinase activation by alpha-lipoic acid; a direct binding measurement would settle whether INSR binds lipoic acid. - go_id: GO:0042619 label: poly-hydroxybutyrate biosynthetic process aspect: BP annotations: - UniProtKB:Q9Z2A7 Dgat1 (mouse, ISO) mechanism: ISO from rat Dgat1 (IMP PMID:23449193) verdict: ANNOTATION_WRONG reason: The source reports raised beta-hydroxybutyrate (ketogenesis) after DGAT1 inhibition; poly-hydroxybutyrate is a prokaryotic storage polymer. - go_id: GO:0045895 label: positive regulation of mating-type specific transcription, DNA-templated aspect: BP annotations: - UniProtKB:A0A0B4J1L1 Ahr (mouse, ISO) - UniProtKB:F6TX41 Ahr (mouse, ISO) - UniProtKB:P30561 Ahr (mouse, ISO) mechanism: ISO from rat Ahr (IDA PMID:9056263) verdict: ANNOTATION_WRONG reason: The source shows AhR-ARNT enhances DRE-driven transcription; mating-type specific transcription is a fungal concept. replacement: GO:0045944 positive regulation of transcription by RNA polymerase II - go_id: GO:0046461 label: neutral lipid catabolic process aspect: BP annotations: - UniProtKB:A0A1L1SQT9 Lipc (mouse, ISO) - UniProtKB:A0A1L1SRU8 Lipc (mouse, ISO) - UniProtKB:P27656 Lipc (mouse, ISO) mechanism: ISO from rat Lipc (IDA PMID:1865764) verdict: TRUE_BUT_GENERAL reason: Hepatic lipase hydrolyses triglycerides. replacement: GO:0019433 triglyceride catabolic process - go_id: GO:0120127 label: response to zinc ion starvation aspect: BP annotations: - UniProtKB:F6ZLZ4 Dpys (mouse, ISO) - UniProtKB:Q9EQF5 Dpys (mouse, ISO) mechanism: ISO from rat Dpys (IDA PMID:7626590) verdict: FLAG_FAILS reason: Rat liver dihydropyrimidinase falls on a zinc-deficient diet; animal biology, low value. - go_id: GO:1905589 label: positive regulation of L-arginine import across plasma membrane aspect: BP annotations: - UniProtKB:A0A5F8MPW1 Agt (mouse, ISO) - UniProtKB:F6UJJ0 Agt (mouse, ISO) - UniProtKB:P11859 Agt (mouse, ISO) mechanism: ISO from rat Agt (IDA PMID:7499219) verdict: FLAG_FAILS reason: Angiotensin-stimulated arginine uptake is a mammalian observation. - go_id: GO:0019255 label: glucose 1-phosphate metabolic process aspect: BP annotations: - UniProtKB:Q91ZJ5 Ugp2 (mouse, ISO) mechanism: ISO from rat Ugp2 (IDA) verdict: FLAG_FAILS reason: UGP2 converts glucose 1-phosphate to UDP-glucose. - go_id: GO:0044377 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding, bending aspect: MF annotations: - UniProtKB:P53568 Cebpg (mouse, ISO) mechanism: ISO from rat Cebpg (IDA PMID:1377818) verdict: FLAG_FAILS reason: Rat IDA for C/EBP DNA binding with bending; animal TF biology. - go_id: GO:0015517 label: galactose:proton symporter activity aspect: MF annotations: - UniProtKB:B0QZL3 Slc45a1 (mouse, ISO) - UniProtKB:Q8BIV7 Slc45a1 (mouse, ISO) - UniProtKB:Q8BIV7 Slc45a1 (mouse, ISS) - UniProtKB:Q9Y2W3 SLC45A1 (human, ISS) mechanism: ISO from rat Slc45a1 (IDA PMID:12417639); ISS verdict: FLAG_FAILS reason: Rat SLC45A1 (PAST-A) is a proton-coupled hexose transporter shown to carry galactose. - go_id: GO:0015743 label: malate transport aspect: BP annotations: - UniProtKB:Q9QZD8 Slc25a10 (mouse, ISO) mechanism: ISO from rat Slc25a10 (IDA PMID:9733776) verdict: FLAG_FAILS reason: The mitochondrial dicarboxylate carrier transports malate. - go_id: GO:0004564 label: beta-fructofuranosidase activity aspect: MF annotations: - UniProtKB:B5THE3 Sis (mouse, ISO) mechanism: ISO from rat Si (IDA PMID:6802834) verdict: ANNOTATION_WRONG reason: Sucrase-isomaltase is sucrose alpha-glucohydrolase (EC 3.2.1.48), as the source states; beta-fructofuranosidase is the invertase class (EC 3.2.1.26). replacement: GO:0004575 sucrose alpha-glucosidase activity - go_id: GO:0015794 label: glycerol-3-phosphate transmembrane transport aspect: BP annotations: - UniProtKB:Q9WU81 Slc37a2 (mouse, ISA) mechanism: ISA from human SLC37A1 (PMID:11112347) verdict: ANNOTATION_WRONG reason: PMID:11112347 named SLC37A1 a putative G3P permease by homology only; SLC37A1/A2 were later shown to be phosphate-linked glucose-6-phosphate antiporters (UniProt FUNCTION). - go_id: GO:0015169 label: glycerol-3-phosphate transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9WU81 Slc37a2 (mouse, ISA) mechanism: ISA from human SLC37A1 (PMID:11112347) verdict: ANNOTATION_WRONG reason: Same homology-only source as GO:0015794. replacement: GO:0061513 glucose 6-phosphate:phosphate antiporter activity - go_id: GO:0031942 label: i-AAA complex aspect: CC annotations: - UniProtKB:F3YDF1 YME1L (fly, ISS) mechanism: ISS from yeast Yme1 verdict: FLAG_FAILS reason: YME1L forms the i-AAA protease in metazoan mitochondria. - go_id: GO:1903806 label: L-isoleucine import across plasma membrane aspect: BP annotations: - UniProtKB:Q9NP91 SLC6A20 (human, ISS) mechanism: ISS from opossum SLC6A20 (PMID:16234310) verdict: UNCERTAIN reason: The opossum orthologue transports neutral amino acids, but human SLC6A20 is described as an imino-acid/glycine transporter (UniProt FUNCTION); a human isoleucine uptake assay would settle the transfer. - go_id: GO:1904679 label: myo-inositol import across plasma membrane aspect: BP annotations: - UniProtKB:P53794 SLC5A3 (human, ISS) mechanism: ISS from mouse Slc5a3 verdict: FLAG_FAILS reason: SMIT1 is the Na+/myo-inositol importer. - go_id: GO:0090374 label: oligopeptide export from mitochondrion aspect: BP annotations: - UniProtKB:Q7KW40 EG:171D11.2 (fly, ISS) mechanism: ISS from yeast Mdl1 verdict: UNCERTAIN reason: Q7KW40 is an uncharacterised fly ABCB half-transporter; peptide export from mitochondria is shown for yeast Mdl1 only. Assigning Q7KW40 to an orthogroup and a metazoan export assay would settle it. - go_id: GO:0000406 label: double-strand/single-strand DNA junction binding aspect: MF annotations: - UniProtKB:Q9TXR4 msh-2 (worm, ISS) mechanism: ISS from yeast Msh2 (PMID:12072462) verdict: FLAG_FAILS reason: MutS-family proteins bind ds/ss junctions; animal DNA repair biology. - go_id: GO:2000639 label: negative regulation of SREBP signaling pathway aspect: BP annotations: - UniProtKB:Q969H0 FBXW7 (human, ISS) mechanism: ISS from Q0VGT7 verdict: FLAG_FAILS reason: 'Consistent with the FBXW7 review (KEEP_AS_NON_CORE): FBXW7 degrades SREBPs.' - go_id: GO:0072670 label: mitochondrial tRNA threonylcarbamoyladenosine modification aspect: BP annotations: - UniProtKB:Q9VWD6 Tcs4 (fly, ISS) mechanism: ISS from yeast Qri7 verdict: FLAG_FAILS reason: Mitochondrial t6A synthesis by OSGEPL1 orthologues is conserved in metazoa. - go_id: GO:0140659 label: cytoskeletal motor regulator activity aspect: MF annotations: - UniProtKB:Q9D3N2 Clxn (mouse, ISO) mechanism: ISO from Ciona calaxin verdict: FLAG_FAILS reason: Calaxin regulates outer-arm dynein in ciliated animals. - go_id: GO:0046495 label: nicotinamide riboside metabolic process aspect: BP annotations: - UniProtKB:Q9VZR0 Nmrk (fly, ISS) mechanism: ISS from yeast Nrk1 verdict: FLAG_FAILS reason: Nicotinamide riboside kinases (NMRK) exist in animals. - go_id: GO:1904564 label: cytosolic [4Fe-4S] assembly scaffold complex aspect: CC annotations: - UniProtKB:Q9VJI9 Nubp1 (fly, ISS) - UniProtKB:Q9VPD2 Nubp2 (fly, ISS) mechanism: ISS from yeast Nbp35/Cfd1 verdict: FLAG_FAILS reason: NUBP1-NUBP2 form the cytosolic Fe-S scaffold in animals. - go_id: GO:0070903 label: mitochondrial tRNA thio-modification aspect: BP annotations: - UniProtKB:Q9VKD3 Nfs1 (fly, ISS) mechanism: ISS from yeast Nfs1 verdict: FLAG_FAILS reason: NFS1 supplies sulfur for mitochondrial tRNA thiolation in metazoa. - go_id: GO:0070485 label: dehydro-D-arabinono-1,4-lactone biosynthetic process aspect: BP annotations: - UniProtKB:Q9VGF1 Dmel\CG3397 (fly, ISS) - UniProtKB:Q9VGF2 Dmel\CG12224 (fly, ISS) - UniProtKB:Q9VGF3 Dmel\CG18547 (fly, ISS) mechanism: ISS from yeast ARA2 verdict: ANNOTATION_WRONG reason: 'Consistent with the CG18547 review (MARK_AS_OVER_ANNOTATED): D-erythroascorbate synthesis is a fungal pathway, and PAINT deliberately limited it to the fungal node; ISS from ARA2 bypasses that.' - go_id: GO:0043682 label: P-type divalent copper transporter activity aspect: MF annotations: - UniProtKB:B1AQ57 Atp7b (mouse, ISO) - UniProtKB:Q04656 ATP7A (human, ISS) - UniProtKB:Q64446 Atp7b (mouse, ISO) mechanism: ISO from human ATP7B; ISS from mouse Atp7a verdict: ANNOTATION_WRONG reason: ATP7A/ATP7B pump Cu(I); the Cu(II) P-type term also carries only_in_taxon Bacteria. Consistent with the ATP7A review (REMOVE). replacement: GO:0140581 P-type monovalent copper transporter activity - go_id: GO:0015146 label: pentose transmembrane transporter activity aspect: MF annotations: - UniProtKB:P13866 SLC5A1 (human, ISS) - UniProtKB:P53794 SLC5A3 (human, ISS) mechanism: ISS from rabbit SGLT1 and dog SMIT verdict: FLAG_FAILS reason: SMIT1 and SGLT1 carry D-xylose as a secondary substrate; pentose absorption is animal biology. - go_id: GO:0015750 label: pentose transmembrane transport aspect: BP annotations: - UniProtKB:P13866 SLC5A1 (human, ISS) - UniProtKB:P53794 SLC5A3 (human, ISS) mechanism: ISS from rabbit SGLT1 and dog SMIT verdict: FLAG_FAILS reason: Same as GO:0015146. - go_id: GO:0031004 label: potassium ion-transporting ATPase complex aspect: CC annotations: - UniProtKB:O60706 ABCC9 (human, ISS) - UniProtKB:Q09428 ABCC8 (human, ISS) - UniProtKB:Q15842 KCNJ8 (human, ISS) mechanism: ISS from rat SUR1/SUR2/Kir6.1 verdict: ANNOTATION_WRONG reason: KATP channels conduct K+ through Kir6 and are not ATP-driven K+ pumps (Kdp-type); consistent with the ABCC8/ABCC9 reviews (MODIFY). replacement: GO:0008282 inward rectifying potassium channel - go_id: GO:0015450 label: protein-transporting ATPase activity aspect: MF annotations: - UniProtKB:A0A1D5RLZ6 Tomm20 (mouse, ISO) - UniProtKB:Q19967 sec-61.G (worm, ISS) - UniProtKB:Q9DCC8 Tomm20 (mouse, ISO) mechanism: ISO from human TOMM20; ISS (sec-61.G) verdict: ANNOTATION_WRONG reason: Neither TOM20 (a presequence receptor) nor Sec61 gamma (a passive channel subunit) hydrolyses NTP to drive transport; consistent with the TOMM20 review, which REMOVEs the human source row. - go_id: GO:1990621 label: ESCRT IV complex aspect: CC annotations: - UniProtKB:Q9W0B3 Vta1 (fly, ISS) - UniProtKB:Q9W0B3 Vta1 (fly, NAS) - UniProtKB:Q9Y162 Vps4 (fly, ISS) - UniProtKB:Q9Y162 Vps4 (fly, NAS) mechanism: ISS from yeast Vta1/Vps4; NAS ComplexPortal verdict: FLAG_FAILS reason: VPS4-VTA1 (LIP5) is conserved in animals. - go_id: GO:0070274 label: RES complex aspect: CC annotations: - UniProtKB:Q8TAD8 SNIP1 (human, NAS) - UniProtKB:Q9BRD0 BUD13 (human, ISS) - UniProtKB:Q9BRD0 BUD13 (human, NAS) - UniProtKB:Q9Y388 RBMX2 (human, NAS) mechanism: ISS from yeast Bud13; NAS ComplexPortal PMID:39068178 verdict: FLAG_FAILS reason: A human RES complex (BUD13, SNIP1, RBMX2) is structurally defined. - go_id: GO:0044403 label: biological process involved in symbiotic interaction aspect: BP annotations: - UniProtKB:P09958 FURIN (human, TAS) mechanism: TAS Reactome R-HSA-9839923 verdict: TRUE_BUT_GENERAL reason: Furin cleaves viral glycoproteins in the host, so the grouping term is not false, but it is a high-level grouping term; a host-specific process term should be chosen. - go_id: GO:0005351 label: carbohydrate:proton symporter activity aspect: MF annotations: - UniProtKB:O95528 SLC2A10 (human, NAS) - UniProtKB:Q9NRM0 SLC2A9 (human, NAS) mechanism: NAS/TAS (UniProt, PINC) verdict: ANNOTATION_WRONG reason: GLUT9 (SLC2A9) and GLUT10 (SLC2A10) are facilitative uniporters, not proton symporters. - go_id: GO:0005351 label: carbohydrate:proton symporter activity aspect: MF annotations: - UniProtKB:Q9NRA2 SLC17A5 (human, TAS) mechanism: TAS PMID:10581036 verdict: TRUE_BUT_GENERAL reason: Sialin is an H+/sialic acid cotransporter. replacement: GO:0015538 sialic acid:proton symporter activity - go_id: GO:0005985 label: sucrose metabolic process aspect: BP annotations: - UniProtKB:P10253 GAA (human, IC) mechanism: IC from GO:0004558 (PMID:9505277) verdict: ANNOTATION_WRONG reason: GAA hydrolyses alpha-1,4/1,6 glucans and maltose, not sucrose; consistent with the GAA review (MARK_AS_OVER_ANNOTATED). - go_id: GO:0008792 label: arginine decarboxylase activity aspect: MF annotations: - UniProtKB:Q96A70 AZIN2 (human, TAS) mechanism: TAS Reactome R-HSA-350598 verdict: ANNOTATION_WRONG reason: 'Consistent with the AZIN2 review (REMOVE): AZIN2 lacks arginine decarboxylase activity.' - go_id: GO:0015802 label: basic amino acid transport aspect: BP annotations: - UniProtKB:Q07837 SLC3A1 (human, TAS) mechanism: TAS PMID:8054986 verdict: FLAG_FAILS reason: Consistent with the SLC3A1 review (ACCEPT). - go_id: GO:0005983 label: starch catabolic process aspect: BP annotations: - UniProtKB:O43451 MGAM (human, TAS) mechanism: TAS PMID:9446624 verdict: FLAG_FAILS reason: Maltase-glucoamylase digests dietary starch in the intestine. - go_id: GO:0016530 label: metallochaperone activity aspect: MF annotations: - UniProtKB:O00244 ATOX1 (human, TAS) mechanism: TAS PMID:15670166 verdict: TRUE_BUT_GENERAL reason: ATOX1 is a Cu(I) chaperone. replacement: GO:0016531 copper chaperone activity - go_id: GO:0033215 label: reductive iron assimilation aspect: BP annotations: - UniProtKB:Q53TN4 CYBRD1 (human, IC) mechanism: IC from GO:0140571 verdict: FLAG_FAILS reason: The definition is generic (surface Fe3+ reduction then uptake), which is what duodenal CYBRD1 does. - go_id: GO:0016896 label: RNA exonuclease activity, producing 5'-phosphomonoesters aspect: MF annotations: - UniProtKB:Q8IU60 DCP2 (human, TAS) mechanism: TAS Reactome R-HSA-429860 verdict: ANNOTATION_WRONG reason: DCP2 is a decapping enzyme releasing m7GDP, not a 5'-exonuclease. replacement: GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity - go_id: GO:0000404 label: heteroduplex DNA loop binding aspect: MF annotations: - UniProtKB:Q01831 XPC (human, TAS) mechanism: TAS PMID:19941824 verdict: FLAG_FAILS reason: XPC recognises helix-distorting lesions and loops in mammalian NER. - go_id: GO:0102039 label: NADH-dependent peroxiredoxin activity aspect: MF annotations: - UniProtKB:P30048 PRDX3 (human, NAS) mechanism: NAS PMID:7733872 verdict: ANNOTATION_WRONG reason: PRDX3 is a thioredoxin-dependent peroxiredoxin; the NADH-dependent term describes the bacterial AhpC/AhpF system, which the source used only for complementation. replacement: GO:0140824 thioredoxin-dependent peroxiredoxin activity - go_id: GO:0008803 label: bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity aspect: MF annotations: - UniProtKB:P50583 NUDT2 (human, TAS) mechanism: TAS PMID:7487923 verdict: ANNOTATION_WRONG reason: Human NUDT2 cleaves Ap4A asymmetrically; consistent with the NUDT2 review (MODIFY). replacement: GO:0004081 bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity supported_by: - reference_id: PMID:7487923 supporting_text: It is unrelated to the enzymes of diadenosine tetraphosphate catabolism found in prokaryotes and fungi. - go_id: GO:0070911 label: global genome nucleotide-excision repair aspect: BP annotations: - UniProtKB:Q6ZNA4 RNF111 (human, TAS) - UniProtKB:Q70EL2 USP45 (human, TAS) mechanism: TAS Reactome R-HSA-5696399 verdict: FLAG_FAILS reason: RNF111 (XPC ubiquitination) and USP45 (ERCC1 deubiquitination) act in human GG-NER. - go_id: GO:0020002 label: host cell plasma membrane aspect: CC annotations: - UniProtKB:Q5T0T0 MARCHF8 (human, NAS) mechanism: NAS PMID:36867660 verdict: ANNOTATION_WRONG reason: Host cell plasma membrane is for symbiont proteins (never_in_taxon Vertebrata); MARCHF8 is a human protein in its own plasma membrane. replacement: GO:0005886 plasma membrane - go_id: GO:0015926 label: glucosidase activity aspect: MF annotations: - UniProtKB:Q13724 MOGS (human, TAS) - UniProtKB:Q8BHN3 Ganab (mouse, ISO) mechanism: TAS PMID:7635146; ISO from human GANAB verdict: TRUE_BUT_GENERAL reason: MOGS is ER glucosidase I and GANAB glucosidase II; specific terms exist (verified for MOGS only). replacement: GO:0004573 Glc3Man9GlcNAc2 oligosaccharide glucosidase activity (MOGS) - go_id: GO:0000452 label: snoRNA guided rRNA 2'-O-methylation aspect: BP annotations: - UniProtKB:Q9VM69 nop5 (fly, NAS) - UniProtKB:Q9W1V3 Fib (fly, NAS) mechanism: NAS ComplexPortal PMID:22065625 verdict: FLAG_FAILS reason: Fibrillarin and Nop5/NOP58 make box C/D snoRNP methylation in animals. - go_id: GO:0015961 label: diadenosine polyphosphate catabolic process aspect: BP annotations: - UniProtKB:O95989 NUDT3 (human, TAS) mechanism: TAS PMID:10419486 verdict: FLAG_FAILS reason: NUDT3/DIPP1 hydrolyses diadenosine polyphosphates. - go_id: GO:0075713 label: establishment of integrated proviral latency aspect: BP annotations: - UniProtKB:P49917 LIG4 (human, TAS) mechanism: TAS Reactome R-HSA-162592 verdict: ANNOTATION_WRONG reason: 'Consistent with the LIG4 review (MARK_AS_OVER_ANNOTATED): host NHEJ circularises unintegrated viral DNA, a dead end, not establishment of latency.' - go_id: GO:0075713 label: establishment of integrated proviral latency aspect: BP annotations: - UniProtKB:O54962 Banf1 (mouse, TAS) mechanism: TAS PMID:11591818 (MGI) verdict: UNCERTAIN reason: The definition includes integration, and BAF blocks autointegration of the pre-integration complex; whether a host factor should carry this viral-process term needs GO host/virus policy and reading PMID:11591818. - go_id: GO:0044650 label: adhesion of symbiont to host cell aspect: BP annotations: - UniProtKB:P09529 INHBB (human, IEA) mechanism: IEA GOC inference from GO:0046789 (TAS PMID:12456957) verdict: ANNOTATION_WRONG reason: Derived from a misuse of "host cell surface receptor binding" (a symbiont term) on activin beta-B; INHBB is a host ligand, not a symbiont adhesin. - go_id: GO:0046521 label: sphingoid catabolic process aspect: BP annotations: - UniProtKB:Q9NYA1 SPHK1 (human, NAS) mechanism: NAS PMID:10863092 verdict: FLAG_FAILS reason: Sphingoid catabolism (via S1P lyase) is animal biology so the flag fails; the SPHK1 review marks the row over-annotated because SPHK1 is mainly a signalling enzyme. - go_id: GO:0009691 label: cytokinin biosynthetic process aspect: BP annotations: - UniProtKB:E9Q8L0 Psg18 (mouse, TAS) - UniProtKB:F6X5B3 Psg18 (mouse, TAS) - UniProtKB:S4R2S1 Psg18 (mouse, TAS) mechanism: TAS PMID:11805154 verdict: ANNOTATION_WRONG reason: '"Cytokinin" (a plant hormone) is a slip for cytokine: the source paper is about PSG17 binding CD9, with PSG-induced anti-inflammatory cytokine secretion as background.' replacement: GO:0001819 positive regulation of cytokine production (if the cytokine claim is kept) - go_id: GO:1901962 label: S-adenosyl-L-methionine transmembrane transport aspect: BP annotations: - UniProtKB:Q9VBN7 (fly, IEA) mechanism: IEA GOC inference from GO:0000095 verdict: FLAG_FAILS reason: The mitochondrial SAM carrier (SLC25A26) exists in animals. - go_id: GO:0019605 label: butyrate metabolic process aspect: BP annotations: - UniProtKB:Q08AH1 ACSM1 (human, NAS) mechanism: NAS PMID:11470804 verdict: FLAG_FAILS reason: ACSM1 activates short/medium-chain acids including butanoate (UniProt RHEA:46172). - go_id: GO:0018874 label: benzoate metabolic process aspect: BP annotations: - UniProtKB:Q08AH1 ACSM1 (human, NAS) mechanism: NAS PMID:11470804 verdict: FLAG_FAILS reason: ACSM1 is a benzoate-CoA ligase (UniProt, PubMed:10434065), the first step of hippurate formation. - go_id: GO:0008794 label: arsenate reductase (glutaredoxin) activity aspect: MF annotations: - UniProtKB:Q9NS18 GLRX2 (human, TAS) mechanism: TAS PMID:11297543, PMID:11397793 verdict: ANNOTATION_WRONG reason: Glutaredoxin is the electron donor for bacterial ArsC, not the reductase; the cloning paper reports GSH-disulfide oxidoreductase activity only. replacement: GO:0015038 glutathione disulfide oxidoreductase activity - go_id: GO:0035822 label: gene conversion aspect: BP annotations: - UniProtKB:Q9H1E3 NUCKS1 (human, NAS) mechanism: NAS PMID:26323318 verdict: FLAG_FAILS reason: NUCKS1 promotes RAD51-mediated homologous recombination (gene conversion). - go_id: GO:0042939 label: tripeptide transport aspect: BP annotations: - UniProtKB:Q17758 pept-2 (worm, IEA) - UniProtKB:Q21219 pept-1 (worm, IEA) - UniProtKB:Q9JIP7 Slc15a1 (mouse, IEA) mechanism: IEA GOC inference from GO:0042937 verdict: FLAG_FAILS reason: PEPT1/PEPT2 transport tripeptides. - go_id: GO:0008995 label: ribonuclease E activity aspect: MF annotations: - UniProtKB:Q12972 PPP1R8 (human, TAS) mechanism: TAS PMID:9153239 verdict: UNCERTAIN reason: A single 1997 report showed the ARD-1 C-terminal peptide of NIPP1 cleaves at RNase E sites in vitro; no later replication or physiological role. Independent confirmation would settle it. - go_id: GO:0003957 label: NAD(P)+ transhydrogenase (Si-specific) activity aspect: MF annotations: - UniProtKB:Q13423 NNT (human, TAS) mechanism: TAS PMID:9524818 verdict: ANNOTATION_WRONG reason: NNT is the proton-translocating (AB-specific) transhydrogenase; the Si-specific term is the soluble bacterial SthA type. replacement: GO:0008750 proton-translocating NAD(P)+ transhydrogenase activity - go_id: GO:0015904 label: tetracycline transmembrane transport aspect: BP annotations: - UniProtKB:Q14728 SLC75A1 (human, IEA) mechanism: IEA GOC inference from GO:0008493 verdict: ANNOTATION_WRONG reason: SLC75A1 is "tetracycline transporter-like" by name only; its curated function is renal organic anion/NSAID transport (UniProt FUNCTION). - go_id: GO:0043033 label: isoamylase complex aspect: CC annotations: - UniProtKB:P35573 AGL (human, TAS) mechanism: TAS PMID:1374391 verdict: ANNOTATION_WRONG reason: 'Consistent with the AGL review (MARK_AS_OVER_ANNOTATED): the isoamylase complex is a starch-debranching complex; AGL is a monomeric glycogen debranching enzyme.' - go_id: GO:0034639 label: L-amino acid efflux transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q09500 ctns-1 (worm, IC) mechanism: IC from GO:0015811 verdict: TRUE_BUT_GENERAL reason: Cystinosin exports L-cystine from lysosomes. replacement: GO:0015184 L-cystine transmembrane transporter activity - go_id: GO:0070406 label: L-glutamine binding aspect: MF annotations: - UniProtKB:P05990 r (fly, IC) mechanism: IC from GO:0004088 verdict: FLAG_FAILS reason: The CPSII domain of rudimentary hydrolyses glutamine. - go_id: GO:0008300 label: isoprenoid catabolic process aspect: BP annotations: - UniProtKB:O09174 Amacr (mouse, TAS) mechanism: TAS PMID:11060344 verdict: FLAG_FAILS reason: AMACR is required for degradation of isoprenoid-derived pristanic acid. - go_id: GO:1903464 label: negative regulation of mitotic cell cycle DNA replication aspect: BP annotations: - UniProtKB:P41182 BCL6 (human, NAS) mechanism: NAS PMID:10490843 verdict: FLAG_FAILS reason: The concept applies to animals; the evidence is an overexpression phenotype (S-phase delay), so the row is weak. - go_id: GO:0061995 label: ATP-dependent protein-DNA complex displacement activity aspect: MF annotations: - UniProtKB:Q80W85 Npm2 (mouse, TAS) mechanism: TAS Reactome R-MMU-9822114 verdict: ANNOTATION_WRONG reason: Nucleoplasmin 2 is an ATP-independent chromatin chaperone. replacement: GO:0140713 histone chaperone activity - go_id: GO:0033768 label: SUMO-targeted ubiquitin ligase complex aspect: CC annotations: - UniProtKB:A0A0B4LHT4 dgrn (fly, IC) - UniProtKB:Q8I0J6 dgrn (fly, IC) - UniProtKB:Q9VNJ0 dgrn (fly, IC) mechanism: IC PMID:21343912 verdict: FLAG_FAILS reason: Degringolade is the fly STUbL; the definition is generic. - go_id: GO:0000354 label: cis assembly of pre-catalytic spliceosome aspect: BP annotations: - UniProtKB:O75643 SNRNP200 (human, IC) - UniProtKB:Q9BUQ8 DDX23 (human, IC) mechanism: IC from GO:0005682 verdict: FLAG_FAILS reason: U5 snRNP proteins act in pre-catalytic spliceosome assembly in humans. - go_id: GO:0043097 label: pyrimidine nucleoside salvage aspect: BP annotations: - UniProtKB:O00142 TK2 (human, TAS) - UniProtKB:Q9NWZ5 UCKL1 (human, TAS) mechanism: TAS Reactome R-HSA-73614 verdict: FLAG_FAILS reason: Consistent with the TK2 and UCKL1 reviews (ACCEPT). - go_id: GO:0120124 label: membrane fusion priming complex aspect: CC annotations: - UniProtKB:O15498 YKT6 (human, NAS) - UniProtKB:O95721 SNAP29 (human, NAS) - UniProtKB:P56962 STX17 (human, NAS) mechanism: NAS ComplexPortal PMID:38340317 verdict: ANNOTATION_WRONG reason: GO:0120124 is the NSF/SNAP-type complex that dissociates cis-SNAREs; the YKT6-STX17-SNAP29 "priming complex" of PMID:38340317 is a SNARE assembly intermediate that uses the same word. replacement: GO:0031201 SNARE complex - go_id: GO:2001208 label: negative regulation of transcription elongation by RNA polymerase I aspect: BP annotations: - UniProtKB:A8DYA3 tou (fly, NAS) - UniProtKB:O46036 CtBP (fly, NAS) - UniProtKB:Q24368 Iswi (fly, NAS) mechanism: NAS ComplexPortal PMID:22426536 verdict: UNCERTAIN reason: The ToRC paper describes Pol II repression and nucleolar truncated Toutatis isoforms; Pol I elongation regulation is not in the abstract. Full text would settle it. - go_id: GO:0035445 label: borate transmembrane transport aspect: BP annotations: - UniProtKB:A2AJN7 Slc4a11 (mouse, IEA) - UniProtKB:A2AJN8 Slc4a11 (mouse, IEA) - UniProtKB:Q8NBS3 SLC4A11 (human, IEA) mechanism: IEA GOC inference from GO:0080139 verdict: UNCERTAIN reason: Borate transport by SLC4A11 rests on one 2004 report and later studies attributed H+/OH-/NH3 transport instead; reading both would settle it. - group: animals_experimental terms: 198 entry_count: 204 verdicts: ANNOTATION_WRONG: 19 DEFER_TO_CURATOR: 102 FLAG_FAILS: 76 TRUE_BUT_GENERAL: 2 UNCERTAIN: 5 summary: 'Of 198 terms (204 entries), 19 entries are ANNOTATION_WRONG, 5 UNCERTAIN, 2 TRUE_BUT_GENERAL, 76 FLAG_FAILS and 102 DEFER_TO_CURATOR; no CONSTRAINT_QUESTIONABLE. Most flags are rare-but-real animal biology (nematode nucleoside hydrolase and phytochelatin synthase, insect trehalose metabolism, urate degradation in non-hominoid mammals) or ordinary eukaryotic processes curated mostly in yeast. The wrong calls are term-choice errors on experimental rows, then copied to orthologs by ISO/ISS/Ensembl projection: a plant- or fungus-defined concept used for an animal observation (spindle pole body, division septum, induced systemic resistance, de novo methionine synthesis, unbranched 1,6-mannan), a reaction with the wrong acceptor or direction (DAO oxidase as quinone dehydrogenase, AKR1B1 glyceraldehyde reduction as oxidation to glycerate, DAXX as ATP-dependent chaperone, L1 nicking endonuclease as type II restriction enzyme), and a misread paper (mannitol used as a paracellular marker, a host factor given a symbiont term, endothelial ''tip cells'' read as cell tip growth).' fetched_pmids: - PMID:8945517 - PMID:28189564 - PMID:25084278 - PMID:27871484 - PMID:34078740 - PMID:18772345 - PMID:11511187 - PMID:19896942 - PMID:11852104 - PMID:15591059 - PMID:26271729 - PMID:16115860 - PMID:1686595 - PMID:10529246 - PMID:9130699 - PMID:12876219 - PMID:22232702 - PMID:14962670 - PMID:22021714 entries: - go_id: GO:0044732 label: mitotic spindle pole body aspect: CC annotations: - UniProtKB:P07911 UMOD (human, IDA, PMID:20172860) mechanism: IDA (MGI) verdict: ANNOTATION_WRONG reason: The spindle pole body is the fungal MTOC (GO only_in_taxon Fungi), so the term cannot apply to a human protein. The paper reports UMOD at mitotic spindle poles, so this is a wrong-term choice; the animal term is mitotic spindle pole. Same call as the first-round triage. replacement: GO:0097431 mitotic spindle pole supported_by: - reference_id: PMID:20172860 supporting_text: UMOD localization at the mitotic spindle poles and colocalization with other ciliary proteins such as nephrocystin-1 and kinesin family member 3A is demonstrated. - go_id: GO:2000142 label: regulation of DNA-templated transcription initiation aspect: BP annotations: - UniProtKB:B2RS91 Rrn3 (mouse, IDA, PMID:8413268) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Rrn3 regulates Pol I transcription initiation; the term applies to animals. - go_id: GO:0051285 label: cell cortex of cell tip aspect: CC annotations: - UniProtKB:G5EDS2 pod-1 (worm, IDA, PMID:9130699) mechanism: IDA (WB) verdict: DEFER_TO_CURATOR reason: Pod-1 at the anterior cortex of the one-cell embryo; 'cell tip' is defined for elongated cells generally (incl. axons). GO:0061802 anterior cell cortex may be the more exact term. - go_id: GO:0110085 label: mitotic actomyosin contractile ring aspect: CC annotations: - UniProtKB:Q9VS45 RhoGEF4 (fly, IDA, PMID:36917931) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: The definition explicitly covers animal cells; a fly RhoGEF at the cytokinetic ring is ordinary. - go_id: GO:0002229 label: defense response to oomycetes aspect: BP annotations: - UniProtKB:P08953 Tl (fly, IMP, PMID:23865688) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Fly Toll and oomycete infection; the Tl review keeps it as non-core. Oomycetes do infect insects. - go_id: GO:0051455 label: spindle attachment to meiosis I kinetochore aspect: BP annotations: - UniProtKB:Q9VUA5 ssp2 (fly, IMP, PMID:26668329) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Animals have meiosis I kinetochore attachment; fly ssp2 IMP. - go_id: GO:0042907 label: xanthine transmembrane transporter activity aspect: MF annotations: - UniProtKB:P10090 w (fly, IMP, PMID:117796) mechanism: IMP (UniProt) verdict: FLAG_FAILS reason: Drosophila White is an ABC transporter of purine pigment precursors (guanine/xanthine-type); the 1979 uptake study is a classic. - go_id: GO:0042906 label: xanthine transport aspect: BP annotations: - UniProtKB:P10090 w (fly, IMP, PMID:117796) mechanism: IMP (UniProt) verdict: FLAG_FAILS reason: Same White transporter row as the MF term; xanthine uptake in fly tissues is real. - go_id: GO:0000001 label: mitochondrion inheritance aspect: BP annotations: - UniProtKB:Q0KHV6 Pink1 (fly, IMP, PMID:30772175) - UniProtKB:Q9VAW5 larp (fly, IMP, PMID:17951964) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Mitochondrial inheritance at division occurs in animals (incl. germline mtDNA selection); Pink1/larp IMP. - go_id: GO:0031126 label: sno(s)RNA 3'-end processing aspect: BP annotations: - UniProtKB:Q9VRX7 Rexo5 (fly, IMP, PMID:29045842) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: snoRNA 3' processing occurs in animals; Rexo5 IMP. - go_id: GO:0030874 label: nucleolar chromatin aspect: CC annotations: - UniProtKB:P30189 Top1 (fly, IDA, PMID:34544118) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: Animal nucleoli have rDNA chromatin; the term fits a fly topoisomerase. - go_id: GO:0034965 label: intronic box C/D snoRNA processing aspect: BP annotations: - UniProtKB:Q8SXD4 stx (fly, IDA, PMID:41548216) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Intronic snoRNA processing occurs in animals; fly stx IDA. - go_id: GO:0035433 label: acetate transmembrane transport aspect: BP annotations: - UniProtKB:A0A0B4LFF4 Targ (fly, IMP, PMID:34107298) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Acetate transport across membranes occurs in animals; Tarag IMP. - go_id: GO:0061776 label: ATP-dependent topological DNA co-entrapment activity aspect: MF annotations: - UniProtKB:Q23243 morc-1 (worm, IDA, PMID:31442422) mechanism: IDA (UniProt) verdict: DEFER_TO_CURATOR reason: MORC-1 compacts DNA by topological entrapment (2019 study); plausible. - go_id: GO:0140727 label: siRNA-mediated pericentric heterochromatin formation aspect: BP annotations: - UniProtKB:P45975 Su(var)3-9 (fly, IMP, PMID:19948966) - UniProtKB:Q9VUQ5 AGO2 (fly, IMP, PMID:19948966) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: siRNA/Argonaute-directed pericentric heterochromatin occurs in flies; Su(var)3-9/AGO2 IMP. - go_id: GO:0019543 label: propionate catabolic process aspect: BP annotations: - UniProtKB:P41999 nhr-10 (worm, IMP, PMID:30625328) - UniProtKB:Q9XXM8 nhr-68 (worm, IMP, PMID:30625328) mechanism: IMP (UniProt) verdict: FLAG_FAILS reason: C. elegans has a vitamin B12-independent propionate shunt; nhr-10/nhr-68 are its transcriptional activators (a regulation term may be more exact, curator's call). - go_id: GO:0009625 label: response to insect aspect: BP annotations: - UniProtKB:A0A6M3Q7I6 IBIN (fly, IEP, PMID:33907186) - UniProtKB:Q09024 ImpL2 (fly, IEP, PMID:38566182) mechanism: IEP (FlyBase) verdict: DEFER_TO_CURATOR reason: Parasitoid wasps are insects; fly genes induced by wasp infection fit (IEP). - go_id: GO:0010114 label: response to red light aspect: BP annotations: - UniProtKB:P13360 gl (fly, IMP, PMID:14960620) - UniProtKB:Q24106 hid (fly, IMP, PMID:14960620) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Flies sense long-wavelength light; gl/hid IMP (hid review UNDECIDED, abstract only). - go_id: GO:1900239 label: regulation of phenotypic switching aspect: BP annotations: - UniProtKB:Q8IZQ8 MYOCD (human, IEA) - UniProtKB:Q8VIM5 Myocd (mouse, IGI, PMID:19578358) mechanism: IEA UniProtKB (Ensembl projection); IGI (BHF-UCL) verdict: FLAG_FAILS reason: GO's phenotypic switching explicitly includes smooth muscle cell phenotypic transitions; myocardin and miR-143/145 control that switch. - go_id: GO:0000772 label: mating pheromone activity aspect: MF annotations: - UniProtKB:Q5FW60 Mup20 (mouse, IDA, PMID:20525243) - UniProtKB:Q5FW60 Mup20 (mouse, IDA, PMID:31996852) mechanism: IDA (MGI); IDA (UniProt) verdict: FLAG_FAILS reason: Darcin (MUP20) is a male mouse sex pheromone that drives female attraction; fits the definition's behavioural response leading to mating. - go_id: GO:0031554 label: regulation of termination of DNA-templated transcription aspect: BP annotations: - UniProtKB:Q18409 rsp-6 (worm, IGI, PMID:18946043) mechanism: IGI (WB) verdict: DEFER_TO_CURATOR reason: Regulation of transcription termination applies to animals; rsp-6 IGI. - go_id: GO:0015123 label: acetate transmembrane transporter activity aspect: MF annotations: - UniProtKB:A0A0B4LFF4 Targ (fly, IMP, PMID:34107298) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Acetate transport in animals; Tarag IMP. - go_id: GO:0008477 label: purine nucleosidase activity aspect: MF annotations: - UniProtKB:Q9XWN7 (worm, EXP, PMID:12777783) - UniProtKB:Q9XWN7 (worm, IDA, PMID:28218438) - UniProtKB:Q9XWN7 (worm, IEA) mechanism: EXP (UniProt); IDA (UniProt); IEA EC:3.2.2.1 verdict: FLAG_FAILS reason: C. elegans carries a genuine nucleoside hydrolase (most animals lack one); directly assayed. - go_id: GO:0035429 label: gluconate transmembrane transport aspect: BP annotations: - UniProtKB:A0A8V0YGT0 SLC26A7 (chicken, IEA) - UniProtKB:Q8R2Z3 Slc26a7 (mouse, IDA, PMID:15591059) - UniProtKB:Q8TE54 SLC26A7 (human, IEA) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt) verdict: FLAG_FAILS reason: The paper ranks gluconate among anions weakly permeant through the SLC26A7 channel; a marginal but real permeability claim (curator's call if it should stand). The Ensembl projections follow it. - go_id: GO:1901195 label: positive regulation of formation of translation preinitiation complex aspect: BP annotations: - UniProtKB:Q9VGN7 Exd2 (fly, IMP, PMID:29335528) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Translation preinitiation complex formation is eukaryotic; Exd2 IMP. - go_id: GO:0008515 label: sucrose transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q9VSV1 Slc45-1 (fly, IDA, PMID:21586609) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: SLC45 transporters are sucrose/H+ symporters; the fly Slc45-1 paper assays sucrose uptake. - go_id: GO:0071042 label: nuclear polyadenylation-dependent mRNA catabolic process aspect: BP annotations: - UniProtKB:A0A1D5NZ09 PNPT1 (chicken, IEA) - UniProtKB:Q8K1R3 Pnpt1 (mouse, IEA) - UniProtKB:Q8K1R3 Pnpt1 (mouse, ISO) - UniProtKB:Q8K1R3 Pnpt1 (mouse, ISS) - UniProtKB:Q8TCS8 PNPT1 (human, IDA, PMID:16934922) mechanism: IDA (UniProt) on human PNPT1; ISO/ISS/IEA projections verdict: ANNOTATION_WRONG reason: PNPT1 is a mitochondrial enzyme and the cited work is on degradation of mitochondrial RNA, so a nuclear polyadenylation-dependent decay term does not fit. The PNPT1 review MODIFYs the IDA to RNA catabolic process; the mouse ISO/ISS/IEA and chicken IEA rows are projections of it. replacement: GO:0006401 RNA catabolic process - go_id: GO:0006566 label: L-threonine metabolic process aspect: BP annotations: - UniProtKB:F6ZSB7 Phgdh (mouse, IMP, PMID:19114063) - UniProtKB:Q61753 Phgdh (mouse, IMP, PMID:19114063) mechanism: IMP (MGI) verdict: DEFER_TO_CURATOR reason: Phgdh knockout perturbs amino acid metabolism; threonine involvement is plausible but indirect, curator's call. - go_id: GO:0044395 label: protein targeting to vacuolar membrane aspect: BP annotations: - UniProtKB:A0A140LIF8 Irgm2 (mouse, IDA, PMID:34078740) mechanism: IDA (UniProt) verdict: ANNOTATION_WRONG reason: The paper places Irgm2 on the Toxoplasma parasitophorous vacuole membrane. In GO that is a symbiont-containing vacuole membrane (GO:0020005), which is not a descendant of vacuolar membrane (GO:0005774, the host's own vacuole). No process term for targeting to a symbiont-containing vacuole exists; the location itself is the supported claim. replacement: GO:0020005 symbiont-containing vacuole membrane (as a CC annotation) supported_by: - reference_id: PMID:34078740 supporting_text: Endogenous Irgm2 expression and localization at Toxoplasma gondii parasitophorous vacuole membrane. - go_id: GO:0097002 label: mitochondrial inner boundary membrane aspect: CC annotations: - UniProtKB:Q9Y171 OXA1L (fly, IMP, PMID:31746672) - UniProtKB:Q9Y171 OXA1L (fly, ISS) mechanism: IMP (FlyBase); ISS (FlyBase) verdict: FLAG_FAILS reason: The inner boundary membrane exists in animal mitochondria; OXA1L localisation there is plausible (ISS row from yeast Oxa1 agrees). - go_id: GO:0005987 label: sucrose catabolic process aspect: BP annotations: - UniProtKB:B5THE3 Sis (mouse, IMP, PMID:34914943) - UniProtKB:B5THE3 Sis (mouse, ISO) - UniProtKB:P14410 SI (human, IDA, PMID:27480812) mechanism: IMP (UniProt); ISO (GO_Central); IDA (UniProt) verdict: FLAG_FAILS reason: Sucrase-isomaltase hydrolyses dietary sucrose in the gut; correct for an animal enzyme. - go_id: GO:0036218 label: dTTP diphosphatase activity aspect: MF annotations: - UniProtKB:O95671 ASMTL (human, EXP, PMID:24210219) - UniProtKB:O95671 ASMTL (human, IEA) mechanism: EXP (UniProt); IEA RHEA:28534 verdict: FLAG_FAILS reason: ASMTL carries a Maf-family dTTP/UTP pyrophosphatase domain; directly assayed. - go_id: GO:0015774 label: polysaccharide transport aspect: BP annotations: - UniProtKB:Q9JJY3 Smpd3 (mouse, IMP, PMID:22383528) mechanism: IMP (MGI) verdict: DEFER_TO_CURATOR reason: Smpd3 (fro/fro) mice and polysaccharide (GAG) secretion; indirect, curator's call. - go_id: GO:0019277 label: UDP-N-acetylgalactosamine biosynthetic process aspect: BP annotations: - UniProtKB:Q9W0P5 Gale (fly, IMP, PMID:22654673) mechanism: IMP (FlyBase) verdict: FLAG_FAILS reason: Gale interconverts UDP-GlcNAc and UDP-GalNAc in animals; correct. - go_id: GO:0045903 label: positive regulation of translational fidelity aspect: BP annotations: - UniProtKB:F7AVE4 Cdk5rap1 (mouse, IGI, PMID:25738458) - UniProtKB:Q8BTW8 Cdk5rap1 (mouse, IGI, PMID:25738458) mechanism: IGI (MGI) verdict: DEFER_TO_CURATOR reason: CDK5RAP1 ms2i6A tRNA modification improves fidelity; mammal IGI. - go_id: GO:0001015 label: snoRNA transcription by RNA polymerase II aspect: BP annotations: - UniProtKB:Q9V629 cuff (fly, IMP, PMID:28420675) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Pol II snoRNA transcription occurs in animals; cuff IMP. - go_id: GO:0006451 label: translational readthrough aspect: BP annotations: - UniProtKB:Q9VSM8 GAPsec (fly, IDA, PMID:18772345) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: The paper shows GAPsec is required for a SECIS-dependent UGA read-through system in flies and mouse cells; the term applies. - go_id: GO:0046938 label: phytochelatin biosynthetic process aspect: BP annotations: - UniProtKB:A5JYS0 pcs-1 (worm, IBA) - UniProtKB:A5JYS0 pcs-1 (worm, IDA, PMID:11313333) - UniProtKB:A5JYS0 pcs-1 (worm, IEA) - UniProtKB:A5JYS0 pcs-1 (worm, IMP, PMID:20221439) mechanism: IBA PANTHER:PTN002124892; IDA (WB); IEA InterPro:IPR007719; IEA ARBA:ARBA00084495; IMP (WB) verdict: FLAG_FAILS reason: C. elegans PCS-1 is a bona fide phytochelatin synthase (pcs-1 mutants are cadmium-hypersensitive); the IBA node (seeded by plant, yeast and worm PCS) and the InterPro/ARBA rows are right too. - go_id: GO:0110044 label: regulation of cell cycle switching, mitotic to meiotic cell cycle aspect: BP annotations: - UniProtKB:Q17684 rpb-6 (worm, IMP, PMID:20419786) mechanism: IMP (UniProt) verdict: DEFER_TO_CURATOR reason: The mitosis-to-meiosis switch in the worm germline is real; rpb-6 IMP. - go_id: GO:0010200 label: response to chitin aspect: BP annotations: - UniProtKB:A0A087WRT7 Ms4a4a (mouse, IMP, PMID:32589266) mechanism: IMP (MGI) verdict: DEFER_TO_CURATOR reason: Mammalian myeloid cells respond to chitin; Ms4a4a IMP. - go_id: GO:0009036 label: type II site-specific deoxyribonuclease activity aspect: MF annotations: - UniProtKB:O00370 (human, IDA, PMID:8945517) mechanism: IDA (UniProt) verdict: ANNOTATION_WRONG reason: Type II site-specific deoxyribonuclease is the restriction-enzyme activity that cuts both strands at a recognition site to give double-stranded fragments. L1 ORF2p carries an APE-like endonuclease that nicks one strand at a loosely preferred target (TTTT/AA); the paper describes nicking, not double-strand restriction cleavage. replacement: GO:0004520 DNA endonuclease activity supported_by: - reference_id: PMID:8945517 supporting_text: Mutations in conserved amino acid residues of L1 EN abolish its nicking activity and eliminate L1 retrotransposition. - go_id: GO:0060567 label: negative regulation of termination of DNA-templated transcription aspect: BP annotations: - UniProtKB:O54943 Per2 (mouse, IDA, PMID:22767893) mechanism: IDA (UniProt) verdict: DEFER_TO_CURATOR reason: PER2 effects on termination; term applies to animals. - go_id: GO:0006849 label: plasma membrane pyruvate transport aspect: BP annotations: - UniProtKB:A0A0B4LFP5 hrm (fly, IDA, PMID:30318245) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: Fly Hermes imports pyruvate across the plasma membrane; correct. - go_id: GO:0045437 label: uridine nucleosidase activity aspect: MF annotations: - UniProtKB:Q9XWN7 (worm, EXP, PMID:12777783) - UniProtKB:Q9XWN7 (worm, IEA) mechanism: EXP (UniProt); IEA EC:3.2.2.3 verdict: FLAG_FAILS reason: Same C. elegans nucleoside hydrolase; uridine is a demonstrated substrate. - go_id: GO:0001100 label: negative regulation of exit from mitosis aspect: BP annotations: - UniProtKB:A0A8V0X8M3 RGCC (chicken, IEA) - UniProtKB:Q9DBX1 Rgcc (mouse, IEA) - UniProtKB:Q9DBX1 Rgcc (mouse, ISO) - UniProtKB:Q9H4X1 RGCC (human, IDA, PMID:17146433) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); IDA (BHF-UCL) verdict: DEFER_TO_CURATOR reason: Exit from mitosis is eukaryotic; RGCC IDA and its projections. - go_id: GO:0006277 label: DNA amplification aspect: BP annotations: - UniProtKB:O16810 Orc1 (fly, IMP, PMID:18711130) mechanism: IMP (FlyBase) verdict: FLAG_FAILS reason: Developmental chorion gene amplification in fly follicle cells is the textbook case; correct. - go_id: GO:0043577 label: chemotropism aspect: BP annotations: - UniProtKB:O76360 egl-4 (worm, IMP, PMID:26434723) mechanism: IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Defined as movement of an organism or part in a chemical gradient; egl-4 IMP in worms (chemotaxis GO:0006935 may be more usual for animals). - go_id: GO:0090173 label: regulation of synaptonemal complex assembly aspect: BP annotations: - UniProtKB:Q9N2V7 him-19 (worm, IMP, PMID:20071466) mechanism: IMP (WB) verdict: DEFER_TO_CURATOR reason: Synaptonemal complex assembly regulation in worm meiosis; him-19 IMP. - go_id: GO:0045128 label: negative regulation of reciprocal meiotic recombination aspect: BP annotations: - UniProtKB:Q9U2M1 dpy-28 (worm, IMP, PMID:18198337) mechanism: IMP (WB) verdict: DEFER_TO_CURATOR reason: Worm condensin (dpy-28) limits crossovers; IMP. - go_id: GO:0071266 label: '''de novo'' L-methionine biosynthetic process' aspect: BP annotations: - UniProtKB:O35490 Bhmt (mouse, ISO) - UniProtKB:Q93088 BHMT (human, IMP, PMID:10529246) mechanism: IMP (UniProt) on human BHMT, ISO (GO_Central) projection to mouse Bhmt verdict: ANNOTATION_WRONG reason: The term is de novo methionine synthesis from aspartate/homoserine, which GO says occurs in plants, bacteria, archaea and fungi and forbids in Mammalia. BHMT regenerates methionine by methylating homocysteine, which is methionine salvage (methionine synthase activity is part_of GO:0071267). The ISO row on mouse Bhmt inherits the same error. replacement: GO:0071267 L-methionine salvage supported_by: - reference_id: PMID:10529246 supporting_text: catalyzes the transfer of an N-methyl group from betaine to homocysteine to produce dimethylglycine and methionine, respectively. - go_id: GO:0043795 label: glyceraldehyde oxidoreductase activity aspect: MF annotations: - UniProtKB:D3YVJ7 Akr1b1 (mouse, ISO) - UniProtKB:P15121 AKR1B1 (human, IDA, PMID:20837989) - UniProtKB:P45376 Akr1b1 (mouse, IEA) - UniProtKB:P45376 Akr1b1 (mouse, ISO) mechanism: IDA (UniProt, PMID:20837989) on human AKR1B1; ISO/IEA projections to mouse Akr1b1 verdict: ANNOTATION_WRONG reason: GO:0043795 is glyceraldehyde oxidation to (R)-glycerate (the archaeal tungsten/molybdenum GAOR reaction). AKR1B1 reduces glyceraldehyde to glycerol with NADPH (UniProt CATALYTIC ACTIVITY RHEA:23592, EC 1.1.1.372), which is glycerol dehydrogenase (NADP+) activity, a term the gene already carries by EXP. The mouse ISO and Ensembl IEA rows are projections of the same human row. replacement: GO:0047956 glycerol dehydrogenase (NADP+) activity - go_id: GO:0034213 label: quinolinate catabolic process aspect: BP annotations: - UniProtKB:A0A8V0X6V9 QPRT (chicken, IBA) - UniProtKB:Q15274 QPRT (human, IBA) - UniProtKB:Q15274 QPRT (human, IDA, PMID:24038671) - UniProtKB:Q15274 QPRT (human, IDA, PMID:3409840) - UniProtKB:Q15274 QPRT (human, IDA, PMID:9473669) - UniProtKB:Q91X91 Qprt (mouse, IBA) - UniProtKB:Q91X91 Qprt (mouse, ISO) mechanism: IBA PANTHER:PTN000789406; IDA (UniProt); IDA (MGI); ISO (MGI); ISO (GO_Central) verdict: FLAG_FAILS reason: QPRT converts quinolinate to nicotinate mononucleotide; the QPRT review ACCEPTs both the IDA and the IBA rows. - go_id: GO:0047934 label: glucose 1-dehydrogenase (NAD+) activity aspect: MF annotations: - UniProtKB:O95479 H6PD (human, IEA) - UniProtKB:O95479 H6PD (human, ISS) - UniProtKB:Q8CFX1 H6pd (mouse, EXP, PMID:4169027) - UniProtKB:Q8CFX1 H6pd (mouse, IEA) mechanism: IEA RHEA:14293; ISS (UniProt); EXP (UniProt) verdict: FLAG_FAILS reason: H6PD's glucose dehydrogenase domain oxidises glucose with NAD+ as well as NADP+; the EXP and its projections are plausible. - go_id: GO:0015771 label: trehalose transport aspect: BP annotations: - UniProtKB:A1Z8N1 Tret1 (fly, IDA, PMID:20035867) - UniProtKB:A1Z8N1 Tret1 (fly, IDA, PMID:34032568) - UniProtKB:Q8MLQ7 pippin (fly, IDA, PMID:33551766) - UniProtKB:Q9VPX2 MFS3 (fly, IEA) mechanism: IDA (FlyBase); IDA (UniProt); IEA GO:0015574 verdict: FLAG_FAILS reason: Insects circulate trehalose; Tret1 and pippin are assayed trehalose transporters (Tret1 review ACCEPTs). The MFS3 IEA follows from its own IDA transporter row. - go_id: GO:0106415 label: muramoyltetrapeptide carboxypeptidase activity aspect: MF annotations: - UniProtKB:Q9VYX7 PGRP-SA (fly, IDA, PMID:15361936) - UniProtKB:Q9VYX7 PGRP-SA (fly, IEA) mechanism: IDA (FlyBase); IEA EC:3.4.17.13; IEA RHEA:48688 verdict: FLAG_FAILS reason: PGRP-SA was reported to have L,D-carboxypeptidase activity on DAP-type peptidoglycan; the EC/RHEA IEA rows follow from it (whether physiological is a curator matter). - go_id: GO:0009682 label: induced systemic resistance aspect: BP annotations: - UniProtKB:F6SPW1 Myd88 (mouse, IMP, PMID:25084278) - UniProtKB:P22366 Myd88 (mouse, IMP, PMID:25084278) mechanism: IMP (MGI) verdict: ANNOTATION_WRONG reason: Induced systemic resistance is the plant response to non-pathogenic rhizobacteria that is independent of salicylic acid signalling; the definition is plant-specific. The paper shows MyD88-deficient mice fail to mount a local inflammatory response to polymicrobial sepsis (cecal ligation and puncture). The parent term defense response to bacterium carries the claim. replacement: GO:0042742 defense response to bacterium supported_by: - reference_id: PMID:25084278 supporting_text: MyD88-deficient mice were susceptible to sepsis because of an impaired local production of chemokines and defective neutrophil recruitment to the infection site. - go_id: GO:1903939 label: regulation of TORC2 signaling aspect: BP annotations: - UniProtKB:Q8BT18 Armh4 (mouse, IDA, PMID:25418727) mechanism: IDA (UniProt) verdict: DEFER_TO_CURATOR reason: ARMH4/UT2 directly binds and inhibits RICTOR; the mouse IDA is sound for animals. - go_id: GO:1903939 label: regulation of TORC2 signaling aspect: BP annotations: - UniProtKB:Q86TY3 ARMH4 (human, ISS) mechanism: ISS (UniProt) from mouse Q8BT18 verdict: TRUE_BUT_GENERAL reason: The ARMH4 review MODIFYs the ISS row to the signed child, since UT2 inhibits mTORC2. replacement: GO:1903940 negative regulation of TORC2 signaling - go_id: GO:0051601 label: exocyst localization aspect: BP annotations: - UniProtKB:A1Z9X0 aPKC (fly, IMP, PMID:24607370) - UniProtKB:P40793 Cdc42 (fly, IMP, PMID:24607370) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Exocyst localisation occurs in animals; aPKC/Cdc42 IMP (Cdc42 review keeps as non-core). - go_id: GO:0160247 label: autophagy cargo adaptor activity aspect: MF annotations: - UniProtKB:P14199 ref(2)P (fly, IDA, PMID:25931115) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: Ref(2)P is the fly p62/SQSTM1 autophagy receptor; correct. - go_id: GO:0051237 label: maintenance of RNA location aspect: BP annotations: - UniProtKB:P37276 Dhc64C (fly, IDA, PMID:16009136) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Dynein maintains localised mRNAs in fly oocytes; correct concept. - go_id: GO:0090153 label: regulation of sphingolipid biosynthetic process aspect: BP annotations: - UniProtKB:Q7KUD4 iPLA2-VIA (fly, IDA, PMID:29909971) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: iPLA2-VIA and sphingolipid synthesis in flies; plausible. - go_id: GO:0071465 label: cellular response to desiccation aspect: BP annotations: - UniProtKB:Q8ITC7 CapaR (fly, IMP, PMID:22253819) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Desiccation responses are real in insects; CapaR IMP. - go_id: GO:0061645 label: endocytic patch aspect: CC annotations: - UniProtKB:Q9V3I2 Rab5 (fly, IDA, PMID:12876219) mechanism: IDA (UniProt) verdict: UNCERTAIN reason: Endocytic patch is the cortical endocytic-site assembly used mainly for yeast actin patches; the cited paper is about Rab5 on synaptic vesicles in fly photoreceptor terminals and reports Rab5 is not needed for endocytic reformation. Which observation was annotated is unclear; the full text settles it, and a synaptic-vesicle or presynaptic endocytic zone term may be intended. - go_id: GO:0010995 label: free ubiquitin chain depolymerization aspect: BP annotations: - UniProtKB:Q9VZU7 Usp5 (fly, IMP, PMID:25152394) mechanism: IMP (FlyBase) verdict: FLAG_FAILS reason: USP5 disassembles unanchored ubiquitin chains; correct for fly Usp5. - go_id: GO:0022611 label: dormancy process aspect: BP annotations: - UniProtKB:P13508 glp-1 (worm, IEA) - UniProtKB:P14585 lin-12 (worm, IEA) - UniProtKB:Q01617 cpo (fly, IMP, PMID:18852464) mechanism: IEA ARBA:ARBA00091893; IMP (FlyBase) verdict: FLAG_FAILS reason: Dormancy includes dauer and diapause; couch potato is a diapause regulator and the glp-1/lin-12 ARBA rows are kept as non-core in their reviews (dauer maintenance/recovery). - go_id: GO:0072666 label: establishment of protein localization to vacuole aspect: BP annotations: - UniProtKB:D3YXE1 Tnfaip3 (mouse, IDA, PMID:18952128) - UniProtKB:D3Z5R6 Tnfaip3 (mouse, IDA, PMID:18952128) - UniProtKB:Q60769 Tnfaip3 (mouse, IDA, PMID:18952128) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: A20 targets TRAF2 to lysosomes (a lytic vacuole in GO); a lysosome-specific localisation term may be more exact. - go_id: GO:0032196 label: transposition aspect: BP annotations: - UniProtKB:P51521 ovo (fly, IMP, PMID:18791225) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: ovo and transposon mobilisation in flies; curator's call. - go_id: GO:0140671 label: ADA complex aspect: CC annotations: - UniProtKB:M9PHZ1 Ada3 (fly, IPI, PMID:30715476) - UniProtKB:Q9VTZ1 Gcn5 (fly, IPI, PMID:30715476) - UniProtKB:Q9W2I4 Sgf29 (fly, IPI, PMID:30715476) mechanism: IPI (ComplexPortal) verdict: DEFER_TO_CURATOR reason: Drosophila has an ADA (Ada2a/Ada3/Gcn5/Sgf29) complex distinct from SAGA/ATAC; ComplexPortal IPI. - go_id: GO:0060966 label: regulation of gene silencing by regulatory ncRNA aspect: BP annotations: - UniProtKB:O62275 wago-4 (worm, IMP, PMID:30728462) mechanism: IMP (UniProt) verdict: DEFER_TO_CURATOR reason: WAGO-4 dosage limits RNAi; the wago-4 review ACCEPTs. - go_id: GO:0046296 label: glycolate catabolic process aspect: BP annotations: - UniProtKB:E1BRR7 HAO1 (chicken, IBA) - UniProtKB:E1BRR7 HAO1 (chicken, IEA) - UniProtKB:Q9UJM8 HAO1 (human, IBA) - UniProtKB:Q9UJM8 HAO1 (human, IDA, PMID:18215067) - UniProtKB:Q9WU19 Hao1 (mouse, IBA) - UniProtKB:Q9WU19 Hao1 (mouse, IEA) - UniProtKB:Q9WU19 Hao1 (mouse, ISO) - UniProtKB:Q9WU19 Hao1 (mouse, ISS) mechanism: IBA PANTHER:PTN008948292; IEA UniProtKB (Ensembl projection); IDA (UniProt); ISO (GO_Central); ISS (UniProt) verdict: FLAG_FAILS reason: Liver HAO1 oxidises glycolate to glyoxylate; the HAO1 review ACCEPTs the IDA, and the IBA/ISO/ISS/IEA rows are sound. - go_id: GO:0050560 label: aspartate-tRNA(Asn) ligase activity aspect: MF annotations: - UniProtKB:A0A8V0Y1V0 DARS2 (chicken, IEA) - UniProtKB:Q6PI48 DARS2 (human, IDA, PMID:15779907) - UniProtKB:Q6PI48 DARS2 (human, IDA, PMID:17384640) - UniProtKB:Q8BIP0 Dars2 (mouse, IEA) - UniProtKB:Q8BIP0 Dars2 (mouse, ISO) mechanism: IDA (BHF-UCL) on human DARS2; ISO/IEA projections to mouse/chicken verdict: ANNOTATION_WRONG reason: GO:0050560 is the non-discriminating Asp-tRNA(Asx) ligase used where Asn-tRNA is made by transamidation; human mitochondria charge tRNA(Asn) directly with NARS2. The DARS2 review MODIFYs both IDA rows to aspartate-tRNA ligase activity; the mouse ISO and Ensembl IEA rows inherit the error. replacement: GO:0004815 aspartate-tRNA ligase activity - go_id: GO:0004845 label: uracil phosphoribosyltransferase activity aspect: MF annotations: - UniProtKB:M9PHI7 kri (fly, IDA, PMID:26271729) - UniProtKB:O61790 (worm, EXP, PMID:19645718) - UniProtKB:O61790 (worm, IEA) - UniProtKB:Q9VRQ1 kri (fly, IDA, PMID:26271729) mechanism: IDA (FlyBase); EXP (UniProt); IEA EC:2.4.2.9; IEA RHEA:13017 verdict: FLAG_FAILS reason: Fly krishah was shown to be an active UPRT required in vivo, overturning the idea that animal UPRTs are inactive; worm O61790 (OPRT/UPRT) has EXP support. - go_id: GO:0016756 label: glutathione gamma-glutamylcysteinyltransferase activity aspect: MF annotations: - UniProtKB:A5JYS0 pcs-1 (worm, EXP, PMID:20221439) - UniProtKB:A5JYS0 pcs-1 (worm, IBA) - UniProtKB:A5JYS0 pcs-1 (worm, IDA, PMID:11313333) - UniProtKB:A5JYS0 pcs-1 (worm, IEA) mechanism: EXP (UniProt); IBA PANTHER:PTN002124892; IDA (WB); IEA InterPro:IPR007719; IEA EC:2.3.2.15; IEA RHEA:17917; IEA ARBA:ARBA00087654 verdict: FLAG_FAILS reason: Same C. elegans PCS-1; the activity is directly assayed and the IBA/InterPro/EC/RHEA/ARBA rows agree. - go_id: GO:0031930 label: mitochondria-nucleus signaling pathway aspect: BP annotations: - UniProtKB:E1C5T1 SLC25A33 (chicken, IEA) - UniProtKB:Q3TZX3 Slc25a33 (mouse, IDA, PMID:17596519) - UniProtKB:Q9BSK2 SLC25A33 (human, IEA) - UniProtKB:Q9BSK2 SLC25A33 (human, ISS) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Retrograde mitochondria-nucleus signalling occurs in animals; SLC25A33 IDA and projections. - go_id: GO:0006030 label: chitin metabolic process aspect: BP annotations: - UniProtKB:Q9BZP6 CHIA (human, NAS, PMID:10548734) - UniProtKB:Q9VW34 serp (fly, IMP, PMID:31108167) mechanism: NAS (UniProt); IMP (FlyBase) verdict: FLAG_FAILS reason: Mammalian AMCase degrades chitin and fly serpentine is a cuticular chitin deacetylase; correct. - go_id: GO:0090154 label: positive regulation of sphingolipid biosynthetic process aspect: BP annotations: - UniProtKB:E2QCD0 Spt-I (fly, IMP, PMID:26395456) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: SPT positively regulating sphingolipid synthesis is odd for the catalytic subunit, but the term applies to animals. - go_id: GO:1990616 label: magnesium ion export from mitochondrion aspect: BP annotations: - UniProtKB:Q9VM51 MME1 (fly, IDA, PMID:26462626) - UniProtKB:Q9VM51 MME1 (fly, IMP, PMID:26462626) mechanism: IDA (FlyBase); IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Mitochondrial Mg2+ export occurs in animals; fly MME1 IDA/IMP. - go_id: GO:1990624 label: guanyl nucleotide exchange factor inhibitor activity aspect: MF annotations: - UniProtKB:Q9VR38 Mon1 (fly, IDA, PMID:37463208) mechanism: IDA (UniProt) verdict: DEFER_TO_CURATOR reason: GEF inhibitor activity applies to animals; the Mon1 review marks it over-annotated (intramolecular autoinhibition). - go_id: GO:1990139 label: protein localization to nuclear periphery aspect: BP annotations: - UniProtKB:Q9VV73 nxf2 (fly, IMP, PMID:34337769) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Protein localisation to nuclear periphery occurs in animals; nxf2 IMP. - go_id: GO:0098653 label: centromere clustering aspect: BP annotations: - UniProtKB:Q9VX37 corolla (fly, IMP, PMID:24913682) - UniProtKB:Q9W3W9 sv2 (fly, IDA, PMID:40744629) - UniProtKB:X2JKX2 corolla (fly, IMP, PMID:24913682) mechanism: IMP (FlyBase); IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Centromere clustering occurs in fly meiosis (corolla) and elsewhere; fine. - go_id: GO:0007107 label: membrane addition at site of cytokinesis aspect: BP annotations: - UniProtKB:Q9W4X9 Zw10 (fly, IMP, PMID:22685323) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Membrane addition at the cleavage furrow occurs in animal cytokinesis; the Zw10 review keeps as non-core. - go_id: GO:0010973 label: positive regulation of division septum assembly aspect: BP annotations: - UniProtKB:Q9N4A7 npp-20 (worm, IMP, PMID:12937276) mechanism: IMP (UniProt) verdict: ANNOTATION_WRONG reason: Animal cells form no division septum (GO only_in_taxon Bacteria/Fungi). The npp-20 review already MODIFYs this row to mitotic cytokinesis (genes/worm/npp-20/npp-20-ai-review.yaml); carried over from the first round. replacement: GO:0000281 mitotic cytokinesis - go_id: GO:0005477 label: pyruvate secondary active transmembrane transporter activity aspect: MF annotations: - UniProtKB:A0A0B4LFP5 hrm (fly, IDA, PMID:30318245) - UniProtKB:O60669 SLC16A7 (human, TAS, PMID:9786900) mechanism: IDA (FlyBase); TAS (PINC) verdict: FLAG_FAILS reason: Fly Hermes and human MCT2 are proton-coupled monocarboxylate transporters of pyruvate; correct. - go_id: GO:0008653 label: lipopolysaccharide metabolic process aspect: BP annotations: - UniProtKB:A0A1Y7VJ47 Aoah (mouse, IDA, PMID:15155618) - UniProtKB:O35298 Aoah (mouse, IDA, PMID:15155618) mechanism: IDA (MGI) verdict: FLAG_FAILS reason: AOAH deacylates LPS in host tissues; correct for a mammalian enzyme. - go_id: GO:0032272 label: negative regulation of protein polymerization aspect: BP annotations: - UniProtKB:Q60930 Vdac2 (mouse, IMP, PMID:12881569) mechanism: IMP (UniProt) verdict: DEFER_TO_CURATOR reason: VDAC2 inhibits BAK oligomerisation; plausible. - go_id: GO:0062132 label: regulation of L-glutamine biosynthetic process aspect: BP annotations: - UniProtKB:Q04688 Ets97D (fly, IMP, PMID:19742324) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Ets97D and glutamine synthesis regulation in flies; plausible. - go_id: GO:0007105 label: cytokinesis, division site positioning aspect: BP annotations: - UniProtKB:Q9V4P1 scra (fly, IMP, PMID:20237160) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Anillin positions the cleavage furrow in animal cells; fine. - go_id: GO:0002131 label: wobble position cytosine ribose methylation aspect: BP annotations: - UniProtKB:Q9VDD9 Trm7-34 (fly, IMP, PMID:31943105) mechanism: IMP (FlyBase) verdict: FLAG_FAILS reason: Trm7-34 2'-O-methylates position 34 of tRNA in flies; correct. - go_id: GO:0008496 label: mannan endo-1,6-alpha-mannosidase activity aspect: MF annotations: - UniProtKB:A0A8V0Y9V3 MAN2B2 (chicken, IEA) - UniProtKB:O54782 Man2b2 (mouse, IEA) - UniProtKB:Q9Y2E5 MAN2B2 (human, IDA, PMID:16115860) mechanism: IDA (MGI) on human MAN2B2; Ensembl IEA projections to mouse/chicken verdict: ANNOTATION_WRONG reason: Mannan endo-1,6-alpha-mannosidase (EC 3.2.1.101) cuts within unbranched 1,6-mannans, a fungal cell-wall polymer absent from animals. MAN2B2 is the lysosomal core-specific exo-alpha1,6-mannosidase that removes the core alpha1-6 mannose of Man3GlcNAc. The mouse and chicken IEA rows are Ensembl projections of the human IDA. replacement: GO:0052767 mannosyl-oligosaccharide 1,6-alpha-mannosidase activity supported_by: - reference_id: PMID:16115860 supporting_text: the former enzyme efficiently cleaved only the alpha1-6mannose residue from Man(3)GlcNAc but not Man(3)GlcNAc(2) or other larger high mannose oligosaccharides - go_id: GO:0043610 label: regulation of carbohydrate utilization aspect: BP annotations: - UniProtKB:A0A0C5B5G6 MT-RNR1 (human, IDA, PMID:25738459) - UniProtKB:Q9JLN9 Mtor (mouse, ISO) mechanism: IDA (UniProt); ISO (GO_Central) verdict: DEFER_TO_CURATOR reason: MOTS-c and mTOR effects on glucose utilisation; both reviews keep as non-core. - go_id: GO:1900079 label: regulation of arginine biosynthetic process aspect: BP annotations: - UniProtKB:Q13286 CLN3 (human, IEA) - UniProtKB:Q13286 CLN3 (human, ISS) - UniProtKB:Q61124 Cln3 (mouse, IMP, PMID:19284480) mechanism: IEA UniProtKB (Ensembl projection); ISS (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Cln3 knockout alters arginine levels; the CLN3 review keeps the projected rows as non-core. - go_id: GO:0008447 label: L-ascorbate oxidase activity aspect: MF annotations: - UniProtKB:Q9VLC3 Mco1 (fly, IDA, PMID:25701385) - UniProtKB:Q9VLC3 Mco1 (fly, IEA) mechanism: IDA (FlyBase); IEA EC:1.10.3.3 verdict: FLAG_FAILS reason: Fly MCO1 was shown to oxidise ascorbate as well as iron; correct. - go_id: GO:0015707 label: nitrite transport aspect: BP annotations: - UniProtKB:A0A087WNR0 Slc11a1 (mouse, IDA, PMID:8529105) - UniProtKB:P41251 Slc11a1 (mouse, IDA, PMID:8529105) - UniProtKB:P49279 SLC11A1 (human, ISS) mechanism: IDA (MGI); ISS (BHF-UCL) verdict: DEFER_TO_CURATOR reason: Nramp1 and nitrite flux in macrophages; plausible, curator's call. - go_id: GO:0090071 label: negative regulation of ribosome biogenesis aspect: BP annotations: - UniProtKB:O08586 Pten (mouse, IMP, PMID:18082964) - UniProtKB:P34611 ncl-1 (worm, IMP, PMID:28853436) - UniProtKB:P34611 ncl-1 (worm, IMP, PMID:9508766) - UniProtKB:Q64364 Cdkn2a (mouse, IDA, PMID:20513429) mechanism: IMP (CACAO); IMP (UniProt); IMP (WB); IDA (UniProt) verdict: DEFER_TO_CURATOR reason: ARF, PTEN and ncl-1 restrain ribosome biogenesis; Pten review keeps as non-core. - go_id: GO:1990626 label: mitochondrial outer membrane fusion aspect: BP annotations: - UniProtKB:A0A8V0Z6S4 NME3 (chicken, IEA) - UniProtKB:Q13232 NME3 (human, IDA, PMID:37584589) - UniProtKB:Q9WV85 Nme3 (mouse, IEA) - UniProtKB:Q9WV85 Nme3 (mouse, ISO) - UniProtKB:Q9WV85 Nme3 (mouse, ISS) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt); ISO (GO_Central); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Mitochondrial outer membrane fusion occurs in animals; NME3 IDA and projections. - go_id: GO:0032160 label: septin filament array aspect: CC annotations: - UniProtKB:E9Q1G8 Septin7 (mouse, IDA, PMID:22232702) - UniProtKB:E9Q9F5 Septin7 (mouse, IDA, PMID:22232702) - UniProtKB:O55131 Septin7 (mouse, IDA, PMID:22232702) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Mouse septin filaments assembling at the T-cell cortex; the definition's examples are fungal spore membranes, so GO:0032156 septin cytoskeleton may be the better fit. - go_id: GO:0003825 label: alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity aspect: MF annotations: - UniProtKB:O45380 tps-2 (worm, IBA) - UniProtKB:O45380 tps-2 (worm, IEA) - UniProtKB:Q7YZT6 tps-1 (worm, IBA) - UniProtKB:Q7YZT6 tps-1 (worm, IEA) - UniProtKB:Q9Y119 Tps1 (fly, IBA) - UniProtKB:Q9Y119 Tps1 (fly, IDA, PMID:22762304) - UniProtKB:Q9Y119 Tps1 (fly, IEA) mechanism: IBA PANTHER:PTN000082164; IEA EC:2.4.1.15; IEA RHEA:18889; IDA (FlyBase) verdict: FLAG_FAILS reason: Insects and nematodes synthesise trehalose with TPS; the Tps1 review ACCEPTs the IDA, IBA and EC rows, and the worm tps-1/tps-2 IBA/EC rows are sound. - go_id: GO:0005998 label: xylulose catabolic process aspect: BP annotations: - UniProtKB:O75191 XYLB (human, TAS, PMID:9763671) - UniProtKB:Q21929 dhs-21 (worm, IDA, PMID:21477590) mechanism: TAS (BHF-UCL); IDA (WB) verdict: FLAG_FAILS reason: XYLB and DHS-21 (L-xylulose reductase) act in the animal glucuronate-xylulose pathway; correct. - go_id: GO:0009403 label: toxin biosynthetic process aspect: BP annotations: - UniProtKB:P00186 Cyp1a2 (mouse, IEA) - UniProtKB:P00186 Cyp1a2 (mouse, ISO) - UniProtKB:P05177 CYP1A2 (human, IDA, PMID:11511187) mechanism: IDA (BHF-UCL) on human CYP1A2; ISO/IEA projections to mouse Cyp1a2 verdict: ANNOTATION_WRONG reason: 'Toxin biosynthesis means an organism making its own toxin. The paper shows CYP1A1/1A2 reductively activate aristolochic acid, a plant nephrotoxin, to DNA-adduct-forming metabolites: that is metabolism of a xenobiotic toxin. The mouse ISO and Ensembl IEA rows project the human row.' replacement: GO:0006805 xenobiotic metabolic process (or GO:0009404 toxin metabolic process) supported_by: - reference_id: PMID:11511187 supporting_text: Aristolochic acid (AA), a naturally occurring nephrotoxin and rodent carcinogen - go_id: GO:0042413 label: carnitine catabolic process aspect: BP annotations: - UniProtKB:P28330 ACADL (human, ISS) - UniProtKB:P51174 Acadl (mouse, IMP, PMID:9861014) mechanism: IMP (BHF-UCL) on mouse Acadl; ISS (BHF-UCL) to human ACADL verdict: ANNOTATION_WRONG reason: Mammals do not degrade carnitine (carnitine catabolism to trimethylamine is bacterial); LCAD dehydrogenates long-chain acyl-CoAs, and Acadl-null mice show altered acylcarnitines because beta-oxidation is blocked. The Acadl review kept this as non-core; it now removes it (2026-11-11), because the term names carnitine breakdown, which LCAD does not do. The human ISS row copies the mouse row. replacement: GO:0006635 fatty acid beta-oxidation - go_id: GO:0015797 label: mannitol transmembrane transport aspect: BP annotations: - UniProtKB:Q8CIW6 Slc26a6 (mouse, IMP, PMID:22021714) - UniProtKB:Q9BXS9 SLC26A6 (human, ISS) mechanism: IMP (UniProt) on mouse Slc26a6; ISS (UniProt) to human SLC26A6 verdict: ANNOTATION_WRONG reason: The cached abstract states that mannitol was used as a marker of paracellular flux across intestine; the paper measures SLC26A6-dependent oxalate secretion, not mannitol transport. The human ISS row copies the mouse row, and the SLC26A6 review already REMOVEs it. replacement: GO:0019532 oxalate transport supported_by: - reference_id: PMID:22021714 supporting_text: We measured transepithelial absorption of [(14)C]oxalate simultaneously with the flux of [(3)H]mannitol, a marker of the paracellular pathway, across intestine from wild-type and Slc26a6-null mice. - go_id: GO:0047724 label: inosine nucleosidase activity aspect: MF annotations: - UniProtKB:Q9XWN7 (worm, EXP, PMID:12777783) - UniProtKB:Q9XWN7 (worm, IDA, PMID:28218438) - UniProtKB:Q9XWN7 (worm, IEA) mechanism: EXP (UniProt); IDA (UniProt); IEA EC:3.2.2.2 verdict: FLAG_FAILS reason: Same C. elegans nucleoside hydrolase; inosine is a demonstrated substrate. - go_id: GO:0034338 label: short-chain carboxylesterase activity aspect: MF annotations: - UniProtKB:P08171 Est-6 (fly, IDA, PMID:28393888) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Est-6 is a fly carboxylesterase assayed directly; short-chain ester hydrolysis is plausible. - go_id: GO:0034338 label: short-chain carboxylesterase activity aspect: MF annotations: - UniProtKB:Q5F2F2 Abhd15 (mouse, IBA) - UniProtKB:Q6UXT9 ABHD15 (human, IBA) mechanism: IBA PANTHER:PTN000082644 verdict: UNCERTAIN reason: 'PTN000082644 is seeded by yeast Eht1/Eeb1 and human ABHD2 (acetylesterase EC 3.1.1.6). ABHD15 has no demonstrated hydrolase activity (UniProt: may regulate adipocyte lipolysis, by similarity); settle by checking whether ABHD15 sits inside the clade below the IBD node or on a diverged branch.' - go_id: GO:0016433 label: rRNA (adenine) methyltransferase activity aspect: MF annotations: - UniProtKB:A0A8V0Z9V7 TRMT61B (chicken, IEA) - UniProtKB:Q7K2B0 (fly, ISS) - UniProtKB:Q9BVS5 TRMT61B (human, IMP, PMID:27631568) mechanism: IEA UniProtKB (Ensembl projection); ISS (FlyBase); IMP (UniProt) verdict: FLAG_FAILS reason: TRMT61B also methylates m1A947 of mitochondrial 16S rRNA (PMID:27631568); fly Rrp8 ISS from yeast Rrp8 is reasonable. - go_id: GO:0000721 label: (R,R)-butanediol dehydrogenase activity aspect: MF annotations: - UniProtKB:Q00796 SORD (human, EXP, PMID:3365415) - UniProtKB:Q00796 SORD (human, IEA) - UniProtKB:Q64442 Sord (mouse, ISO) mechanism: EXP (UniProt); IEA EC:1.1.1.4; IEA RHEA:24340; ISO (GO_Central) verdict: FLAG_FAILS reason: Sorbitol dehydrogenase oxidises (R,R)-butanediol (EXP); correct. - go_id: GO:0089721 label: phosphoenolpyruvate transmembrane transporter activity aspect: MF annotations: - UniProtKB:Q3KQZ1 SLC25A35 (human, IEA) - UniProtKB:Q3KQZ1 SLC25A35 (human, ISS) - UniProtKB:Q5SWT3 Slc25a35 (mouse, IDA, PMID:41850288) mechanism: IEA UniProtKB (Ensembl projection); ISS (UniProt); IDA (UniProt) verdict: FLAG_FAILS reason: SLC25A35 was assayed as a PEP carrier; mitochondrial carrier, plausible in animals. - go_id: GO:0071264 label: positive regulation of translational initiation in response to starvation aspect: BP annotations: - UniProtKB:Q9P2K8 EIF2AK4 (human, ISS) - UniProtKB:Q9QZ05 Eif2ak4 (mouse, IDA, PMID:10655230) - UniProtKB:Q9QZ05 Eif2ak4 (mouse, IMP, PMID:16121183) mechanism: ISS (UniProt); IDA (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: GCN2-dependent translation control in starvation occurs in mammals; the EIF2AK4 review ACCEPTs. - go_id: GO:0016074 label: sno(s)RNA metabolic process aspect: BP annotations: - UniProtKB:A0A140LIR6 Fbl (mouse, IMP, PMID:14612397) - UniProtKB:P35550 Fbl (mouse, IMP, PMID:14612397) mechanism: IMP (MGI) verdict: DEFER_TO_CURATOR reason: Fibrillarin is a box C/D snoRNP component; fine. - go_id: GO:0044374 label: sequence-specific DNA binding, bending aspect: MF annotations: - UniProtKB:P35710 Sox5 (mouse, IDA, PMID:8078769) mechanism: IDA (UniProt) verdict: FLAG_FAILS reason: SOX HMG boxes bend DNA sequence-specifically; correct. - go_id: GO:0000740 label: nuclear membrane fusion aspect: BP annotations: - UniProtKB:P00356 GAPDH (chicken, IMP, PMID:12651855) mechanism: IMP (AgBase) verdict: DEFER_TO_CURATOR reason: Nuclear envelope reassembly involves membrane fusion in animal cells; chicken GAPDH IMP. - go_id: GO:0009202 label: deoxyribonucleoside triphosphate biosynthetic process aspect: BP annotations: - UniProtKB:P08879 awd (fly, IDA, PMID:1320004) mechanism: IDA (UniProt) verdict: FLAG_FAILS reason: Awd is the main larval NDPK; the awd review ACCEPTs this IDA. - go_id: GO:1905866 label: positive regulation of Atg1/ULK1 kinase complex assembly aspect: BP annotations: - UniProtKB:P12370 Pka-C1 (fly, IMP, PMID:29606597) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Atg1/ULK1 complex regulation in fly autophagy; PKA IMP. - go_id: GO:0010777 label: meiotic mismatch repair involved in reciprocal meiotic recombination aspect: BP annotations: - UniProtKB:Q24595 Xpc (fly, IGI, PMID:25188408) mechanism: IGI (FlyBase) verdict: DEFER_TO_CURATOR reason: Meiotic mismatch repair in fly recombination; Xpc IGI. - go_id: GO:0031024 label: interphase microtubule organizing center assembly aspect: BP annotations: - UniProtKB:Q9I7U5 Cnb (fly, IMP, PMID:23354166) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Interphase centrosome/MTOC assembly occurs in animals; Centrobin IMP. - go_id: GO:0004780 label: sulfate adenylyltransferase (ADP) activity aspect: MF annotations: - UniProtKB:D8FRQ0 dcs-1 (worm, IDA, PMID:19896942) - UniProtKB:G5EFS4 dcs-1 (worm, IDA, PMID:19896942) mechanism: IDA (WB) verdict: FLAG_FAILS reason: C. elegans DcpS phosphorolyses APS to ADP (the reverse of the GO reaction); directly assayed HIT-family side activity. - go_id: GO:0090139 label: mitochondrial chromosome packaging aspect: BP annotations: - UniProtKB:Q94234 hmg-5 (worm, IMP, PMID:21258070) mechanism: IMP (WB) verdict: FLAG_FAILS reason: HMG-5 is the worm TFAM-like mtDNA packaging protein; correct. - go_id: GO:1990477 label: MTREC complex aspect: CC annotations: - UniProtKB:A0A8V0YAQ2 ZFC3H1 (chicken, IEA) - UniProtKB:F7A3J9 Zfc3h1 (mouse, ISO) - UniProtKB:O60293 ZFC3H1 (human, IDA, PMID:27871484) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); IDA (UniProt) verdict: DEFER_TO_CURATOR reason: ZFC3H1 is the human ortholog of S. pombe Red1 and part of the PAXT connection; GO notes MTREC is related to human complexes and has no PAXT term (ontology gap, not a wrong annotation). - go_id: GO:1904931 label: MCM complex binding aspect: MF annotations: - UniProtKB:Q7KW09 Gcna (fly, IDA, PMID:31839537) - UniProtKB:Q8K203 Neil3 (mouse, ISS) - UniProtKB:Q8TAT5 NEIL3 (human, ISS) mechanism: IDA (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Gcna and NEIL3 bind MCM; fine. - go_id: GO:0030682 label: symbiont-mediated perturbation of host defenses aspect: BP annotations: - UniProtKB:A2ADZ6 Kpna6 (mouse, IMP, PMID:28189564) - UniProtKB:F8WHL4 Kpna6 (mouse, IMP, PMID:28189564) - UniProtKB:O35345 Kpna6 (mouse, IMP, PMID:28189564) mechanism: IMP (MGI) verdict: ANNOTATION_WRONG reason: A symbiont process term on a host protein, breaking GO's never_in_taxon Vertebrata constraint. The paper shows mouse importin-alpha7 is a host factor that H7N9 influenza uses for replication; the host protein does not perturb its own defences. The host-side term for a pro-viral host factor is positive regulation of viral genome replication. replacement: GO:0045070 positive regulation of viral genome replication supported_by: - reference_id: PMID:28189564 supporting_text: importin-α7 knockout mice presented reduced pulmonary virus titers and lung lesions as well as enhanced survival rates compared to wild-type mice. - go_id: GO:0032806 label: carboxy-terminal domain protein kinase complex aspect: CC annotations: - UniProtKB:A1Z8B6 Mat1 (fly, IDA, PMID:11447116) - UniProtKB:O76513 CycH (fly, IDA, PMID:11447116) - UniProtKB:Q24216 Cdk7 (fly, IDA, PMID:11447116) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: Fly CAK (Cdk7/CycH/Mat1) is the RNA Pol II CTD kinase of TFIIH; correct. - go_id: GO:0043617 label: cellular response to sucrose starvation aspect: BP annotations: - UniProtKB:Q9VVK5 Adgf-A (fly, IMP, PMID:20940317) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Sugar starvation responses in flies; Adgf-A IMP. - go_id: GO:0009855 label: determination of bilateral symmetry aspect: BP annotations: - UniProtKB:A0ACM8PYB6 Ilp8 (fly, IMP, PMID:22556250) - UniProtKB:Q62148 Aldh1a2 (mouse, IMP, PMID:15731404) mechanism: IMP (FlyBase); IMP (MGI) verdict: DEFER_TO_CURATOR reason: Bilateral symmetry (fluctuating asymmetry, left-right somites) is an animal trait; Ilp8/Aldh1a2 IMP. - go_id: GO:0045148 label: tripeptide aminopeptidase activity aspect: MF annotations: - UniProtKB:P09960 LTA4H (human, EXP, PMID:11675384) - UniProtKB:P09960 LTA4H (human, EXP, PMID:11917124) - UniProtKB:P09960 LTA4H (human, EXP, PMID:20813919) - UniProtKB:P09960 LTA4H (human, EXP, PMID:24591641) - UniProtKB:P09960 LTA4H (human, EXP, PMID:9395533) - UniProtKB:P09960 LTA4H (human, IEA) - UniProtKB:P24527 Lta4h (mouse, EXP, PMID:1881903) - UniProtKB:P24527 Lta4h (mouse, EXP, PMID:20813919) - UniProtKB:P24527 Lta4h (mouse, IEA) - UniProtKB:P24527 Lta4h (mouse, ISO) mechanism: EXP (UniProt); IEA EC:3.4.11.4; ISO (GO_Central) verdict: FLAG_FAILS reason: LTA4H has a well-characterised aminopeptidase activity on tripeptides (e.g. Pro-Gly-Pro); correct. - go_id: GO:0015138 label: fumarate transmembrane transporter activity aspect: MF annotations: - UniProtKB:A0A8V1AM47 SLC13A2 (chicken, IBA) - UniProtKB:A0A8V1AM47 SLC13A2 (chicken, IEA) - UniProtKB:Q13183 SLC13A2 (human, IBA) - UniProtKB:Q13183 SLC13A2 (human, IDA, PMID:10894787) - UniProtKB:Q13183 SLC13A2 (human, IEA) - UniProtKB:Q9ES88 Slc13a2 (mouse, IBA) - UniProtKB:Q9ES88 Slc13a2 (mouse, IEA) - UniProtKB:Q9ES88 Slc13a2 (mouse, ISO) - UniProtKB:Q9ES88 Slc13a2 (mouse, ISS) mechanism: IBA PANTHER:PTN008496849; IEA UniProtKB (Ensembl projection); IDA (UniProt); ISO (GO_Central); ISS (UniProt) verdict: FLAG_FAILS reason: NaDC1 transports C4-dicarboxylates including fumarate; the IDA, IBA and projections are sound. - go_id: GO:0032329 label: serine transport aspect: BP annotations: - UniProtKB:A2ALH6 Slc38a5 (mouse, ISO) - UniProtKB:Q3U1J0 Slc38a5 (mouse, IBA) - UniProtKB:Q3U1J0 Slc38a5 (mouse, IEA) - UniProtKB:Q3U1J0 Slc38a5 (mouse, ISO) - UniProtKB:Q8WUX1 SLC38A5 (human, IBA) - UniProtKB:Q8WUX1 SLC38A5 (human, IMP, PMID:11243884) mechanism: ISO (GO_Central); IBA PANTHER:PTN002741896; IEA UniProtKB (Ensembl projection); IMP (ARUK-UCL) verdict: FLAG_FAILS reason: SNAT5 transports serine among neutral amino acids; correct. - go_id: GO:0051595 label: response to methylglyoxal aspect: BP annotations: - UniProtKB:E9PXF9 Sin3a (mouse, IDA, PMID:17670746) - UniProtKB:E9Q2L1 Sin3a (mouse, IDA, PMID:17670746) - UniProtKB:Q60520 Sin3a (mouse, IDA, PMID:17670746) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Sin3a and methylglyoxal response in mammals; plausible. - go_id: GO:0051997 label: 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity aspect: MF annotations: - UniProtKB:Q283N4 Urad (mouse, IBA) - UniProtKB:Q283N4 Urad (mouse, IDA, PMID:16462750) - UniProtKB:Q283N4 Urad (mouse, IEA) mechanism: IBA PANTHER:PTN000044713; IDA (MGI); IEA EC:4.1.1.97; IEA RHEA:26301; IEA ARBA:ARBA00089513 verdict: FLAG_FAILS reason: Non-hominoid mammals degrade urate via urate oxidase, HIUase and OHCU decarboxylase (Urad); correct. - go_id: GO:0019402 label: galactitol metabolic process aspect: BP annotations: - UniProtKB:Q9R0N0 Galk1 (mouse, IMP, PMID:10915771) mechanism: IMP (MGI) verdict: DEFER_TO_CURATOR reason: Galk1-null mice accumulate galactitol via aldose reductase; involvement of GALK1 itself is indirect, curator's call. - go_id: GO:0140696 label: (S)-2-hydroxyglutarate dehydrogenase (quinone) activity aspect: MF annotations: - UniProtKB:Q9VJ28 L2HGDH (fly, IDA, PMID:42203459) mechanism: IDA (FlyBase) verdict: FLAG_FAILS reason: L2HGDH is a FAD/quinone-linked L-2-hydroxyglutarate dehydrogenase; correct. - go_id: GO:0044774 label: mitotic DNA integrity checkpoint signaling aspect: BP annotations: - UniProtKB:A0A0N4SVW0 Setmar (mouse, ISO) - UniProtKB:Q53H47 SETMAR (human, IBA) - UniProtKB:Q53H47 SETMAR (human, IMP, PMID:18790802) - UniProtKB:Q80UJ9 Setmar (mouse, ISO) mechanism: ISO (GO_Central); IBA PANTHER:PTN002917896; IMP (UniProt) verdict: DEFER_TO_CURATOR reason: SETMAR and the mitotic DNA damage checkpoint; IMP plus projections, and the IBA node is seeded by SETMAR itself. - go_id: GO:0051728 label: cell cycle switching, mitotic to meiotic cell cycle aspect: BP annotations: - UniProtKB:A0A8V0YQQ0 RBM46 (chicken, IEA) - UniProtKB:P86049 Rbm46 (mouse, IMP, PMID:36001654) - UniProtKB:Q8TBY0 RBM46 (human, IEA) - UniProtKB:Q8TBY0 RBM46 (human, ISS) mechanism: IEA UniProtKB (Ensembl projection); IMP (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Rbm46 is required for the meiotic switch in mouse germ cells; fine. - go_id: GO:0052574 label: UDP-galactose biosynthetic process aspect: BP annotations: - UniProtKB:E2QCV4 Galk (fly, IMP, PMID:27562100) - UniProtKB:Q9VMA2 Galt (fly, IMP, PMID:27562100) - UniProtKB:Q9W0P5 Gale (fly, IMP, PMID:20519568) - UniProtKB:Q9W0P5 Gale (fly, IMP, PMID:22654673) mechanism: IMP (FlyBase) verdict: FLAG_FAILS reason: The Leloir pathway (Galk, Galt, Gale) makes UDP-galactose in flies; correct. - go_id: GO:0042131 label: thiamine phosphate phosphatase activity aspect: MF annotations: - UniProtKB:P15309 ACP3 (human, IEA) - UniProtKB:P15309 ACP3 (human, ISS) - UniProtKB:Q8CE08 Acp3 (mouse, IMP, PMID:18940592) mechanism: IEA UniProtKB (Ensembl projection); ISS (CAFA); IMP (UniProt) verdict: FLAG_FAILS reason: Prostatic acid phosphatase is the thiamine monophosphatase of DRG neurons; correct, and the projections follow. - go_id: GO:0070202 label: regulation of establishment of protein localization to chromosome aspect: BP annotations: - UniProtKB:Q14159 SPIDR (human, IBA) - UniProtKB:Q14159 SPIDR (human, IDA, PMID:23509288) - UniProtKB:Q8BGX7 Spidr (mouse, IBA) - UniProtKB:Q8BGX7 Spidr (mouse, IEA) - UniProtKB:Q8BGX7 Spidr (mouse, ISO) - UniProtKB:Q8BGX7 Spidr (mouse, ISS) mechanism: IBA PANTHER:PTN002154254; IDA (UniProt); IEA UniProtKB (Ensembl projection); ISO (GO_Central); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: SPIDR scaffolds BLM/RAD51 on chromatin; IDA, IBA (seeded by SPIDR) and projections are consistent. - go_id: GO:0001112 label: DNA-templated transcription open complex formation aspect: BP annotations: - UniProtKB:Q7Z7C8 TAF8 (human, IDA, PMID:14580349) - UniProtKB:Q9EQH4 Taf8 (mouse, ISO, PMID:14580349) mechanism: IDA (MGI); ISO (MGI) verdict: DEFER_TO_CURATOR reason: TAF8/TFIID and open complex formation; fine for animals. - go_id: GO:0004037 label: allantoicase activity aspect: MF annotations: - UniProtKB:Q8N6M5 ALLC (human, IEA) mechanism: IEA InterPro IPR005164/IPR015908 and Ensembl projection from mouse verdict: ANNOTATION_WRONG reason: Human ALLC is a probable inactive allantoicase and allantoicase activity is absent from mammals; the ALLC review REMOVEs the electronic rows. The InterPro family mapping is right for active members but not for this pseudoenzyme. - go_id: GO:0004037 label: allantoicase activity aspect: MF annotations: - UniProtKB:Q9JHX6 Allc (mouse, IDA, PMID:11852104) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Recombinant mouse allantoicase was assayed and showed activity with low substrate affinity; whether this is function (enzyme-specificity tiers) is for the curator, since the authors attribute the in vivo loss of activity to low affinity and expression. supported_by: - reference_id: PMID:11852104 supporting_text: We propose that the loss of allantoicase activity in mouse is due to a low substrate affinity and to a reduced expression level of the enzyme. - go_id: GO:0004037 label: allantoicase activity aspect: MF annotations: - UniProtKB:Q9JHX6 Allc (mouse, IEA) mechanism: IEA InterPro IPR005164/IPR015908 verdict: UNCERTAIN reason: The mouse InterPro row is concordant with the recombinant assay but the authors report no allantoicase activity in mouse tissue; settle by deciding whether the in vitro activity is physiological. - go_id: GO:0046520 label: sphingoid biosynthetic process aspect: BP annotations: - UniProtKB:Q8BG54 Sptlc3 (mouse, ISO) - UniProtKB:Q9NUV7 SPTLC3 (human, IDA, PMID:19648650) mechanism: ISO (MGI); IDA (MGI) verdict: FLAG_FAILS reason: SPTLC3 is a serine palmitoyltransferase subunit making sphingoid bases; correct. - go_id: GO:0004754 label: saccharopine dehydrogenase (NAD+, L-lysine-forming) activity aspect: MF annotations: - UniProtKB:Q9VLX0 LKRSDH (fly, IDA, PMID:18695041) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Fly LKR/SDH was assayed directly; whether it uses NADH as reported is a curator matter. - go_id: GO:0004754 label: saccharopine dehydrogenase (NAD+, L-lysine-forming) activity aspect: MF annotations: - UniProtKB:Q9UDR5 AASS (human, ISS) mechanism: ISS (FlyBase) from fly Q9VLX0 verdict: ANNOTATION_WRONG reason: 'Lateral cofactor error, not a lineage error: the AASS review MODIFYs this ISS row to the NADP+ form, since human LKR is NADPH-dependent and the fly donor assay does not exclude NADPH.' replacement: GO:0047130 saccharopine dehydrogenase (NADP+, L-lysine-forming) activity - go_id: GO:0031078 label: histone H3K14 deacetylase activity, hydrolytic mechanism aspect: MF annotations: - UniProtKB:Q99N13 Hdac9 (mouse, IMP, PMID:21708950) - UniProtKB:Q9UKV0 HDAC9 (human, ISS, PMID:21708950) mechanism: IMP (ARUK-UCL); ISS (ARUK-UCL) verdict: DEFER_TO_CURATOR reason: Class IIa HDAC9 and H3K14 deacetylation; weak intrinsic activity is debated, curator's call. - go_id: GO:1990545 label: mitochondrial thiamine pyrophosphate transmembrane transport aspect: BP annotations: - UniProtKB:A0A0B4K7P9 Tpc2 (fly, ISS, PMID:20121944) - UniProtKB:Q0KI86 Tpc1 (fly, IGI, PMID:20121944) mechanism: ISS (FlyBase); IGI (FlyBase) verdict: DEFER_TO_CURATOR reason: Fly Tpc1/Tpc2 mitochondrial TPP carriers; IGI with yeast and ISS. - go_id: GO:0090052 label: regulation of pericentric heterochromatin formation aspect: BP annotations: - UniProtKB:Q7KVA6 mu2 (fly, IMP, PMID:25934801) - UniProtKB:Q9W061 mu2 (fly, IMP, PMID:25934801) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: mu2 regulates pericentric heterochromatin in flies; fine. - go_id: GO:0071311 label: cellular response to acetate aspect: BP annotations: - UniProtKB:Q9VRL4 Ir64a (fly, IDA, PMID:23804096) - UniProtKB:Q9W365 Ir8a (fly, IDA, PMID:23804096) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Ir64a/Ir8a mediate acid (acetate) sensing in flies; fine. - go_id: GO:0070199 label: establishment of protein localization to chromosome aspect: BP annotations: - UniProtKB:G5EDA3 hcp-4 (worm, IMP, PMID:11402065) - UniProtKB:P34470 hcp-3 (worm, IMP, PMID:11402065) - UniProtKB:P34470 hcp-3 (worm, TAS, PMID:11402065) mechanism: IMP (UniProt); TAS (UniProt) verdict: DEFER_TO_CURATOR reason: HCP-3/HCP-4 loading on worm holocentric chromosomes; fine. - go_id: GO:0008718 label: D-amino-acid dehydrogenase activity aspect: MF annotations: - UniProtKB:A0A8V0ZIU2 DAO (chicken, IEA) - UniProtKB:P14920 DAO (human, IEA) - UniProtKB:P18894 Dao (mouse, IMP, PMID:1686595) mechanism: IMP (UniProt) on mouse Dao; Ensembl IEA projections to human/chicken verdict: ANNOTATION_WRONG reason: GO:0008718 is the quinone-linked bacterial D-amino-acid dehydrogenase (DadA). Mammalian DAO is a peroxisomal FAD oxidase that uses O2 and makes H2O2; the cited mutant mice lack D-amino-acid oxidase activity. The IEA rows on human and chicken DAO are Ensembl projections of this mouse row. replacement: GO:0003884 D-amino-acid oxidase activity supported_by: - reference_id: PMID:1686595 supporting_text: These results suggest that the mutant mice synthesize the D-amino-acid oxidase protein and integrate it into peroxisomes, though it is a nonfunctional enzyme. - go_id: GO:0046052 label: UTP catabolic process aspect: BP annotations: - UniProtKB:A0A8V0ZPA6 ENTPD7 (chicken, IEA) - UniProtKB:Q3TCT4 Entpd7 (mouse, IEA) - UniProtKB:Q3TCT4 Entpd7 (mouse, ISO) - UniProtKB:Q3TCT4 Entpd7 (mouse, ISS) - UniProtKB:Q9NQZ7 ENTPD7 (human, IDA, PMID:11278936) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); ISS (UniProt); IDA (UniProt) verdict: FLAG_FAILS reason: ENTPD7 hydrolyses UTP; correct. - go_id: GO:0016444 label: somatic cell DNA recombination aspect: BP annotations: - UniProtKB:Q6A028 Swap70 (mouse, IDA, PMID:9642267) - UniProtKB:Q9VGN7 Exd2 (fly, IMP, PMID:18056975) mechanism: IDA (MGI); IMP (FlyBase) verdict: FLAG_FAILS reason: Class-switch recombination (SWAP-70) and fly somatic recombination are animal somatic recombination; correct. - go_id: GO:0034196 label: acylglycerol transport aspect: BP annotations: - UniProtKB:Q7KTG2 Apoltp (fly, IMP, PMID:22844248) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Lipophorin transfer particle moves acylglycerols in fly haemolymph; fine. - go_id: GO:0140496 label: gamma-tubulin complex binding aspect: MF annotations: - UniProtKB:Q9V877 sub (fly, IDA, PMID:30087124) mechanism: IDA (FlyBase) verdict: DEFER_TO_CURATOR reason: Subito binding to gamma-tubulin complexes; fine. - go_id: GO:0120243 label: 2-iminopropanoate deaminase activity aspect: MF annotations: - UniProtKB:P52758 RIDA (human, EXP, PMID:22094463) - UniProtKB:P52758 RIDA (human, IEA) - UniProtKB:P52760 Rida (mouse, IEA) - UniProtKB:P52760 Rida (mouse, ISO) - UniProtKB:P52760 Rida (mouse, ISS) mechanism: EXP (UniProt); IEA RHEA:40671; ISO (GO_Central); ISS (UniProt) verdict: FLAG_FAILS reason: RIDA is the conserved Rid family enamine/imine deaminase; human EXP and its projections are sound. - go_id: GO:0061163 label: endoplasmic reticulum polarization aspect: BP annotations: - UniProtKB:A0A8V0ZT01 SHTN1 (chicken, IEA) - UniProtKB:A0MZ66 SHTN1 (human, IEA) - UniProtKB:A0MZ66 SHTN1 (human, ISS) - UniProtKB:Q8K2Q9 Shtn1 (mouse, IMP, PMID:23864681) mechanism: IEA UniProtKB (Ensembl projection); ISS (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Shootin-1 and ER polarisation in neurons; IMP plus projections. - go_id: GO:0032038 label: myosin II heavy chain binding aspect: MF annotations: - UniProtKB:P08590 MYL3 (human, NAS, PMID:16675844) - UniProtKB:P12829 MYL4 (human, NAS, PMID:16675844) - UniProtKB:Q9VJ14 mib2 (fly, IPI, PMID:18216171) mechanism: NAS (BHF-UCL); IPI (FlyBase) verdict: FLAG_FAILS reason: Myosin essential light chains bind the myosin II heavy chain (NAS); the mib2 IPI is ordinary binding. - go_id: GO:0035543 label: positive regulation of SNARE complex assembly aspect: BP annotations: - UniProtKB:A0A8V0XZX1 SNCA (chicken, IEA) - UniProtKB:O55042 Snca (mouse, ISO) - UniProtKB:P37840 SNCA (human, IDA, PMID:20798282) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); IDA (CACAO) verdict: FLAG_FAILS reason: Alpha-synuclein chaperones SNARE complex assembly (Burre et al. 2010); the SNCA review ACCEPTs. - go_id: GO:0018063 label: cytochrome c-heme linkage aspect: BP annotations: - UniProtKB:G3UXK7 Hccs (mouse, ISO) - UniProtKB:P53701 HCCS (human, IDA, PMID:23150584) - UniProtKB:P53702 Hccs (mouse, ISO) mechanism: ISO (GO_Central); IDA (UniProt) verdict: FLAG_FAILS reason: HCCS attaches heme to cytochrome c in animal mitochondria; correct. - go_id: GO:0032377 label: regulation of intracellular lipid transport aspect: BP annotations: - UniProtKB:F1N859 TMEM97 (chicken, IBA) - UniProtKB:F1N859 TMEM97 (chicken, IEA) - UniProtKB:Q5BJF2 TMEM97 (human, IBA) - UniProtKB:Q5BJF2 TMEM97 (human, IMP, PMID:27378690) - UniProtKB:Q8VD00 Tmem97 (mouse, IBA) - UniProtKB:Q8VD00 Tmem97 (mouse, IEA) - UniProtKB:Q8VD00 Tmem97 (mouse, ISO) - UniProtKB:Q8VD00 Tmem97 (mouse, ISS) mechanism: IBA PANTHER:PTN001260854; IEA UniProtKB (Ensembl projection); IMP (UniProt); ISO (GO_Central); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: TMEM97 (sigma-2) and intracellular cholesterol transport; IMP, IBA and projections consistent. - go_id: GO:0071618 label: lysophosphatidylethanolamine acyltransferase activity aspect: MF annotations: - UniProtKB:A0A8V0ZLA3 LPGAT1 (chicken, IEA) - UniProtKB:Q91YX5 Lpgat1 (mouse, IDA, PMID:35131264) - UniProtKB:Q92604 LPGAT1 (human, IEA) - UniProtKB:Q92604 LPGAT1 (human, ISS) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt); ISS (UniProt) verdict: FLAG_FAILS reason: LPGAT1 acylates lysophosphatidylethanolamine; the LPGAT1 review ACCEPTs the projected rows. - go_id: GO:0140013 label: meiotic nuclear division aspect: BP annotations: - UniProtKB:A0A8V0Y4A4 RAB24 (chicken, IEA) - UniProtKB:P35290 Rab24 (mouse, IMP, PMID:31496367) - UniProtKB:Q969Q5 RAB24 (human, IEA) - UniProtKB:Q969Q5 RAB24 (human, ISS) mechanism: IEA UniProtKB (Ensembl projection); IMP (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Rab24 in mouse oocyte meiosis; the RAB24 review keeps the projections as non-core. - go_id: GO:0097080 label: plasma membrane selenite transport aspect: BP annotations: - UniProtKB:A0A8V0XRS0 SLC39A8 (chicken, IEA) - UniProtKB:Q91W10 Slc39a8 (mouse, IDA, PMID:27166256) - UniProtKB:Q91W10 Slc39a8 (mouse, IEA) - UniProtKB:Q91W10 Slc39a8 (mouse, ISO) - UniProtKB:Q9C0K1 SLC39A8 (human, IDA, PMID:27166256) - UniProtKB:Q9C0K1 SLC39A8 (human, IEA) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt); ISO (GO_Central) verdict: FLAG_FAILS reason: ZIP8 was shown to take up selenite; correct. - go_id: GO:2001246 label: negative regulation of phosphatidylcholine biosynthetic process aspect: BP annotations: - UniProtKB:D6RE48 Lpcat1 (mouse, IDA, PMID:20018880) - UniProtKB:D6RFA8 Lpcat1 (mouse, IDA, PMID:20018880) - UniProtKB:Q3TFD2 Lpcat1 (mouse, IDA, PMID:20018880) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Lpcat1 IDA; curator's call on the sign. - go_id: GO:1990893 label: mitotic chromosome centromere condensation aspect: BP annotations: - UniProtKB:G5EEH9 npp-10 (worm, IMP, PMID:28122936) - UniProtKB:Q9BKT9 npp-13 (worm, IMP, PMID:28122936) - UniProtKB:Q9N4A7 npp-20 (worm, IMP, PMID:28122936) mechanism: IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Centromere condensation in worm mitosis; the npp-20 review marks this over-annotated (downstream of HCP-4 import). - go_id: GO:0019203 label: carbohydrate phosphatase activity aspect: MF annotations: - UniProtKB:A0A8V0XX26 EPM2A (chicken, IEA) - UniProtKB:O95278 EPM2A (human, EXP, PMID:16901901) - UniProtKB:O95278 EPM2A (human, IDA, PMID:25538239) - UniProtKB:O95278 EPM2A (human, IEA) - UniProtKB:O95278 EPM2A (human, TAS) - UniProtKB:Q9WUA5 Epm2a (mouse, IDA, PMID:18040046) - UniProtKB:Q9WUA5 Epm2a (mouse, IEA) - UniProtKB:Q9WUA5 Epm2a (mouse, IMP, PMID:18040046) - UniProtKB:Q9WUA5 Epm2a (mouse, ISO) - UniProtKB:Q9WUA5 Epm2a (mouse, ISS) mechanism: IEA InterPro:IPR045204; IEA ARBA:ARBA00028086; EXP (Reactome); IDA (UniProt); IEA UniProtKB (Ensembl projection); TAS (Reactome); IDA (MGI); IMP (MGI); ISO (GO_Central); ISS (UniProt) verdict: FLAG_FAILS reason: Laforin is a glucan phosphatase; the EPM2A review ACCEPTs the EXP, IDA, TAS and IEA rows. - go_id: GO:0080183 label: response to photooxidative stress aspect: BP annotations: - UniProtKB:A0A8V0XHF7 NXNL1 (chicken, IEA) - UniProtKB:Q8VC33 Nxnl1 (mouse, IMP, PMID:25596499) - UniProtKB:Q96CM4 NXNL1 (human, IEA) - UniProtKB:Q96CM4 NXNL1 (human, ISS) mechanism: IEA UniProtKB (Ensembl projection); IMP (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: Photooxidative stress in the retina; Nxnl1 IMP and projections. - go_id: GO:0043470 label: regulation of carbohydrate catabolic process aspect: BP annotations: - UniProtKB:E1BRR6 SCARB2 (chicken, IEA) - UniProtKB:O35114 Scarb2 (mouse, IEA) - UniProtKB:O35114 Scarb2 (mouse, IMP, PMID:18022370) - UniProtKB:O35114 Scarb2 (mouse, ISO) - UniProtKB:Q14108 SCARB2 (human, IEA) - UniProtKB:Q14108 SCARB2 (human, IMP, PMID:18022370) mechanism: IEA UniProtKB (Ensembl projection); IMP (ARUK-UCL); ISO (GO_Central) verdict: DEFER_TO_CURATOR reason: LIMP-2 delivers glucocerebrosidase to lysosomes; the SCARB2 review keeps as non-core (indirect). - go_id: GO:0019866 label: organelle inner membrane aspect: CC annotations: - UniProtKB:Q8WWR8 NEU4 (human, IDA, PMID:14962670) mechanism: IDA (UniProt) verdict: UNCERTAIN reason: The abstract says NEU4 associates with 'inner cell membranes', which means intracellular membranes, not the inner bilayer of an organelle envelope; the term may be a misreading. Reading the full-text localisation figures settles it (NEU4 is reported elsewhere on lysosomes and mitochondria). replacement: GO:0012505 endomembrane system (if the figures show only intracellular membranes) supported_by: - reference_id: PMID:14962670 supporting_text: Immunofluorescence staining and Western blot analysis demonstrated the association of NEU4 with the inner cell membranes. - go_id: GO:0019866 label: organelle inner membrane aspect: CC annotations: - UniProtKB:A0A8V1A0C4 NEU4 (chicken, IEA) - UniProtKB:Q8BZL1 Neu4 (mouse, IEA) - UniProtKB:Q8BZL1 Neu4 (mouse, ISO) - UniProtKB:Q8BZL1 Neu4 (mouse, ISS) mechanism: ISO/ISS/IEA from human NEU4 verdict: UNCERTAIN reason: Projections (ISO/ISS/Ensembl IEA) of the human IDA; they stand or fall with it. - go_id: GO:0016793 label: triphosphoric monoester hydrolase activity aspect: MF annotations: - UniProtKB:Q5ZJL9 SAMHD1 (chicken, ISS) - UniProtKB:Q60710 Samhd1 (mouse, IDA, PMID:29379009) - UniProtKB:Q9Y3Z3 SAMHD1 (human, IEA) mechanism: ISS (UniProt); IDA (UniProt); IEA UniProtKB (Ensembl projection) verdict: FLAG_FAILS reason: SAMHD1 is a dNTP triphosphohydrolase; correct. - go_id: GO:0090547 label: response to low humidity aspect: BP annotations: - UniProtKB:Q86BF9 Obp59a (fly, IMP, PMID:30230472) mechanism: IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Humidity sensing in flies; Obp59a IMP. - go_id: GO:0050017 label: L-3-cyanoalanine synthase activity aspect: MF annotations: - UniProtKB:O45679 cysl-2 (worm, IDA, PMID:24100226) - UniProtKB:O45679 cysl-2 (worm, IEA) mechanism: IDA (WB); IEA EC:4.4.1.9; IEA RHEA:17821; IEA ARBA:ARBA00043396 verdict: FLAG_FAILS reason: C. elegans CYSL-2 is a bona fide cyanoalanine synthase used in cyanide detoxification; correct. - go_id: GO:0072585 label: xanthosine nucleotidase activity aspect: MF annotations: - UniProtKB:Q9XWN7 (worm, EXP, PMID:12777783) mechanism: EXP (UniProt) verdict: FLAG_FAILS reason: Same C. elegans nucleoside hydrolase; xanthosine is a demonstrated substrate. - go_id: GO:0005476 label: carnitine:O-acyl-L-carnitine antiporter activity aspect: MF annotations: - UniProtKB:O43772 SLC25A20 (human, EXP, PMID:9399886) - UniProtKB:O43772 SLC25A20 (human, TAS) - UniProtKB:Q9Z2Z6 Slc25a20 (mouse, ISO) mechanism: EXP (Reactome); TAS (Reactome); ISO (GO_Central) verdict: FLAG_FAILS reason: SLC25A20 is the carnitine/acylcarnitine carrier; the SLC25A20 review ACCEPTs both rows. - go_id: GO:1905325 label: regulation of meiosis I spindle assembly checkpoint aspect: BP annotations: - UniProtKB:O95229 ZWINT (human, ISS) - UniProtKB:Q9CQU5 Zwint (mouse, IMP, PMID:26486467) mechanism: ISS (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Meiosis I spindle checkpoint in mouse oocytes; Zwint IMP and ISS. - go_id: GO:0098718 label: serine import across plasma membrane aspect: BP annotations: - UniProtKB:O35874 Slc1a4 (mouse, IDA, PMID:11030592) - UniProtKB:Q5SSP3 Slc1a4 (mouse, IDA, PMID:11030592) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: ASCT1 imports serine; fine. - go_id: GO:0033750 label: ribosome localization aspect: BP annotations: - UniProtKB:A1ZAB5 clu (fly, IPI, PMID:26834020) - UniProtKB:Q9VEP0 bdwf (fly, IMP, PMID:37047316) mechanism: IPI (FlyBase); IMP (FlyBase) verdict: DEFER_TO_CURATOR reason: Clueless binds ribosomes at mitochondria; fine. - go_id: GO:0032033 label: myosin II light chain binding aspect: MF annotations: - UniProtKB:Q9NB04 Patj (fly, IDA, PMID:23128243) - UniProtKB:Q9VJ14 mib2 (fly, IPI, PMID:18216171) mechanism: IDA (FlyBase); IPI (FlyBase) verdict: DEFER_TO_CURATOR reason: Patj/mib2 binding to myosin II light chain; fine. - go_id: GO:1904688 label: regulation of cytoplasmic translational initiation aspect: BP annotations: - UniProtKB:D0Z5N4 gcn-2 (worm, IGI, PMID:22719267) - UniProtKB:D0Z5N4 gcn-2 (worm, IMP, PMID:23692540) - UniProtKB:Q19192 pek-1 (worm, IGI, PMID:22719267) mechanism: IGI (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: GCN-2 and PEK-1 regulate cytoplasmic translation initiation; both worm reviews ACCEPT. - go_id: GO:0048308 label: organelle inheritance aspect: BP annotations: - UniProtKB:H2L067 mex-3 (worm, IMP, PMID:8861905) - UniProtKB:Q95R07 mex-3 (worm, IMP, PMID:8861905) mechanism: IMP (WB) verdict: DEFER_TO_CURATOR reason: mex-3 and P-granule/organelle partitioning in worm embryos; curator's call. - go_id: GO:0061573 label: actin filament bundle retrograde transport aspect: BP annotations: - UniProtKB:A0MZ66 SHTN1 (human, ISS) - UniProtKB:Q8K2Q9 Shtn1 (mouse, ISO) - UniProtKB:Q8K2Q9 Shtn1 (mouse, ISS) - UniProtKB:Q8SX68 Naus (fly, IMP, PMID:31164339) mechanism: ISS (UniProt); ISO (GO_Central); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: Shootin-1/Naus and retrograde actin flow; IMP plus projections. - go_id: GO:0001156 label: TFIIIC-class transcription factor complex binding aspect: MF annotations: - UniProtKB:F1NUX4 MTOR (chicken, IEA) - UniProtKB:P42345 MTOR (human, IDA, PMID:20543138) - UniProtKB:Q9JLN9 Mtor (mouse, IEA) - UniProtKB:Q9JLN9 Mtor (mouse, ISO) mechanism: IEA UniProtKB (Ensembl projection); IDA (UniProt); ISO (GO_Central) verdict: DEFER_TO_CURATOR reason: mTOR binds TFIIIC; the Mtor review keeps as non-core. - go_id: GO:0000247 label: C-8 sterol isomerase activity aspect: MF annotations: - UniProtKB:A2AC29 Ebp (mouse, IDA, PMID:8798407) - UniProtKB:A2AC29 Ebp (mouse, IMP, PMID:10391218) - UniProtKB:A2AC29 Ebp (mouse, ISO) - UniProtKB:P70245 Ebp (mouse, IBA) - UniProtKB:P70245 Ebp (mouse, IDA, PMID:8798407) - UniProtKB:P70245 Ebp (mouse, IEA) - UniProtKB:P70245 Ebp (mouse, IMP, PMID:10391218) - UniProtKB:P70245 Ebp (mouse, ISO) - UniProtKB:Q15125 EBP (human, IBA) - UniProtKB:Q15125 EBP (human, IEA) - UniProtKB:Q15125 EBP (human, ISS) mechanism: IDA (MGI); IMP (MGI); ISO (GO_Central); IBA PANTHER:PTN000368006; IEA UniProtKB (Ensembl projection); ISS (UniProt) verdict: FLAG_FAILS reason: The EBP review keeps these rows as non-core because human EBP isomerises fecosterol in substrate assays (PMID:12133002); the physiological activity is GO:0047750 cholestenol delta-isomerase. - go_id: GO:1902985 label: mitotic pre-replicative complex assembly aspect: BP annotations: - UniProtKB:A0A8V0XQ29 CDT1 (chicken, IEA) - UniProtKB:Q8R4E9 Cdt1 (mouse, IEA) - UniProtKB:Q8R4E9 Cdt1 (mouse, ISO) - UniProtKB:Q9H211 CDT1 (human, IDA, PMID:11125146) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); IDA (UniProt) verdict: DEFER_TO_CURATOR reason: CDT1 loads MCM; the CDT1 review ACCEPTs. - go_id: GO:1904291 label: positive regulation of mitotic DNA damage checkpoint aspect: BP annotations: - UniProtKB:A2ASW6 Map3k20 (mouse, ISO) - UniProtKB:Q9ESL4 Map3k20 (mouse, IEA) - UniProtKB:Q9ESL4 Map3k20 (mouse, ISO) - UniProtKB:Q9ESL4 Map3k20 (mouse, ISS) - UniProtKB:Q9NYL2 MAP3K20 (human, IDA, PMID:15342622) mechanism: ISO (GO_Central); IEA UniProtKB (Ensembl projection); ISS (UniProt); IDA (UniProt) verdict: DEFER_TO_CURATOR reason: MAP3K20 phosphorylates CHEK2; the MAP3K20 review keeps as non-core. - go_id: GO:0010610 label: regulation of mRNA stability involved in response to stress aspect: BP annotations: - UniProtKB:A0A8V1A3J6 IGF2BP1 (chicken, IEA) - UniProtKB:O88477 Igf2bp1 (mouse, IEA) - UniProtKB:O88477 Igf2bp1 (mouse, ISO) - UniProtKB:O88477 Igf2bp1 (mouse, ISS) - UniProtKB:Q9NZI8 IGF2BP1 (human, IMP, PMID:17101699) mechanism: IEA UniProtKB (Ensembl projection); ISO (GO_Central); ISS (UniProt); IMP (UniProt) verdict: DEFER_TO_CURATOR reason: IGF2BP1 stabilises mRNAs under stress; fine. - go_id: GO:0140665 label: ATP-dependent H3-H4 histone complex chaperone activity aspect: MF annotations: - UniProtKB:A0A8V0XAB0 (chicken, IEA) - UniProtKB:O35613 Daxx (mouse, IDA, PMID:20651253) - UniProtKB:Q9UER7 DAXX (human, IDA, PMID:20504901) - UniProtKB:Q9UER7 DAXX (human, IDA, PMID:20651253) mechanism: IDA (GO_Central) on human DAXX and mouse Daxx; Ensembl IEA to chicken verdict: ANNOTATION_WRONG reason: DAXX is an H3.3-H4 chaperone but has no ATPase; in both papers the ATP-driven step belongs to its partner ATRX (an SNF2 remodeler). The ATP-dependent child is wrong for DAXX; the parent term fits. The rows look like a GO_Central remap of old chaperone annotations to the ATP-dependent class. replacement: GO:0000510 H3-H4 histone complex chaperone activity supported_by: - reference_id: PMID:20651253 supporting_text: Recombinant Daxx assembles H3.3/H4 tetramers on DNA templates, and the ATRX-Daxx complex catalyzes the deposition and remodeling of H3.3-containing nucleosomes. - go_id: GO:0140129 label: histone H3K56ac reader activity aspect: MF annotations: - UniProtKB:G3UYF2 Pou5f1 (mouse, IDA, PMID:23798425) - UniProtKB:G3UZG9 Pou5f1 (mouse, IDA, PMID:23798425) - UniProtKB:P20263 Pou5f1 (mouse, IDA, PMID:23798425) mechanism: IDA (MGI) verdict: DEFER_TO_CURATOR reason: Oct4 binding H3K56ac; curator's call. - go_id: GO:0001962 label: alpha-1,3-galactosyltransferase activity aspect: MF annotations: - UniProtKB:P38649 Abo (mouse, ISO) - UniProtKB:Q3V1N9 A3galt2 (mouse, IGI, PMID:22875802) - UniProtKB:Q3V1N9 A3galt2 (mouse, ISO) - UniProtKB:Z4YLB0 Abo (mouse, ISO) mechanism: ISO (GO_Central); IGI (MGI); ISO (MGI) verdict: FLAG_FAILS reason: A3galt2 (iGb3 synthase) and ABO are alpha-1,3-galactosyltransferases in mammals; correct. - go_id: GO:0051229 label: meiotic spindle disassembly aspect: BP annotations: - UniProtKB:G5EGK8 let-92 (worm, IMP, PMID:17218259) - UniProtKB:O44740 mei-2 (worm, NAS, PMID:10809666) - UniProtKB:P34808 mei-1 (worm, IMP, PMID:23918937) - UniProtKB:P34808 mei-1 (worm, NAS, PMID:10809666) mechanism: IMP (WB); NAS (ComplexPortal) verdict: DEFER_TO_CURATOR reason: Katanin and PP2A disassemble worm meiotic spindles; fine. - go_id: GO:0048532 label: anatomical structure arrangement aspect: BP annotations: - UniProtKB:F6WAS0 Rac1 (mouse, IMP, PMID:20016102) - UniProtKB:P63001 Rac1 (mouse, IMP, PMID:20016102) mechanism: IMP (MGI) verdict: FLAG_FAILS reason: A generic anatomical term that applies to animals; nothing lineage-specific. - go_id: GO:0120531 label: prenyl diphosphate synthase activity aspect: MF annotations: - UniProtKB:Q9V9Z3 qless (fly, IMP, PMID:20889762) - UniProtKB:Q9V9Z3 qless (fly, TAS, PMID:39864756) - UniProtKB:Q9VP87 Pdss2 (fly, TAS, PMID:39864756) mechanism: IMP (FlyBase); TAS (FlyBase) verdict: FLAG_FAILS reason: Qless/PDSS2 make the polyprenyl tail of ubiquinone; correct. - go_id: GO:0009932 label: cell tip growth aspect: BP annotations: - UniProtKB:A0A8V0YSM5 EDN2 (chicken, IEA) - UniProtKB:P20800 EDN2 (human, IEA) - UniProtKB:P22389 Edn2 (mouse, IDA, PMID:24043815) mechanism: IDA (MGI) on mouse Edn2; Ensembl IEA projections to human/chicken verdict: ANNOTATION_WRONG reason: Cell tip growth is growth at the tip of a single polarised cell (root hair, pollen tube, hypha). The paper is about endothelial 'tip cells', a cell state at the front of a vascular sprout, which Edn2 overexpression in the retina increases while it inhibits angiogenesis non-cell-autonomously. The human and chicken IEA rows are Ensembl projections of this mouse IDA. replacement: GO:0016525 negative regulation of angiogenesis (candidate; read full text for the exact claim) supported_by: - reference_id: PMID:24043815 supporting_text: Edn2 overexpression leads to overproduction of endothelial tip cells by both morphologic and molecular criteria. - go_id: GO:0120242 label: 2-iminobutanoate deaminase activity aspect: MF annotations: - UniProtKB:P52758 RIDA (human, EXP, PMID:22094463) - UniProtKB:P52758 RIDA (human, IEA) - UniProtKB:P52758 RIDA (human, TAS) - UniProtKB:P52760 Rida (mouse, IEA) - UniProtKB:P52760 Rida (mouse, ISO) - UniProtKB:P52760 Rida (mouse, ISS) - UniProtKB:Q9V3W0 UK114 (fly, ISS) mechanism: EXP (UniProt); IEA RHEA:39975; TAS (Reactome); ISO (GO_Central); ISS (UniProt); ISS (FlyBase) verdict: FLAG_FAILS reason: RIDA is the conserved Rid family enamine/imine deaminase; human EXP, Reactome TAS and projections are sound, and fly UK114 ISS from B. subtilis RidA is within the same family. - go_id: GO:1900542 label: regulation of purine nucleotide metabolic process aspect: BP annotations: - UniProtKB:A0A8V0XGG6 LACC1 (chicken, IBA) - UniProtKB:A0A8V0XGG6 LACC1 (chicken, IEA) - UniProtKB:Q8BZT9 Lacc1 (mouse, IBA) - UniProtKB:Q8BZT9 Lacc1 (mouse, IMP, PMID:31978345) - UniProtKB:Q8IV20 LACC1 (human, IBA) - UniProtKB:Q8IV20 LACC1 (human, IEA) - UniProtKB:Q8IV20 LACC1 (human, ISS) mechanism: IBA PANTHER:PTN001255556; IEA UniProtKB (Ensembl projection); IMP (UniProt); ISS (UniProt) verdict: DEFER_TO_CURATOR reason: LACC1 purine metabolism in macrophages; IMP, IBA (seeded by mouse Lacc1) and projections consistent. - go_id: GO:0015574 label: trehalose transmembrane transporter activity aspect: MF annotations: - UniProtKB:A1Z8N1 Tret1 (fly, IDA, PMID:20035867) - UniProtKB:A1Z8N1 Tret1 (fly, IDA, PMID:34032568) - UniProtKB:Q8MLQ7 pippin (fly, IDA, PMID:33551766) - UniProtKB:Q9VPX2 MFS3 (fly, IDA, PMID:33551766) mechanism: IDA (UniProt); IDA (FlyBase) verdict: FLAG_FAILS reason: Tret1, pippin and MFS3 are assayed insect trehalose transporters; the Tret1 review ACCEPTs. - go_id: GO:0002220 label: innate immune response activating cell surface receptor signaling pathway aspect: BP annotations: - UniProtKB:Q8N149 LILRA2 (human, IDA, PMID:27572839) mechanism: IDA (UniProt) verdict: DEFER_TO_CURATOR reason: LILRA2 is an activating immune receptor; never_in_taxon Fungi is not broken. - go_id: GO:0016122 label: xanthophyll metabolic process aspect: BP annotations: - UniProtKB:Q99NF1 Bco2 (mouse, IMP, PMID:25701869) mechanism: IMP (MGI) verdict: FLAG_FAILS reason: BCO2 cleaves xanthophylls such as lutein and zeaxanthin; correct. - go_id: GO:1990359 label: stress response to zinc ion aspect: BP annotations: - UniProtKB:O17003 natc-1 (worm, IGI, PMID:25330323) - UniProtKB:O17003 natc-1 (worm, IMP, PMID:25330323) mechanism: IGI (WB); IMP (WB) verdict: DEFER_TO_CURATOR reason: Worm natc-1 and zinc stress; fine. - go_id: GO:0000234 label: phosphoethanolamine N-methyltransferase activity aspect: MF annotations: - UniProtKB:Q22993 pmt-2 (worm, IEA) - UniProtKB:Q23552 pmt-1 (worm, IDA, PMID:17313371) - UniProtKB:Q23552 pmt-1 (worm, IEA) mechanism: IEA EC:2.1.1.103; IDA (WB); IEA ARBA:ARBA00098314 verdict: FLAG_FAILS reason: C. elegans makes phosphocholine via PMT-1/PMT-2 phosphoethanolamine methyltransferases; correct. - go_id: GO:0051410 label: detoxification of nitrogen compound aspect: BP annotations: - UniProtKB:Q5VT66 MTARC1 (human, NAS, PMID:20861021) - UniProtKB:Q969Z3 MTARC2 (human, NAS, PMID:20861021) - UniProtKB:Q9VGT0 Ugt35B1 (fly, IMP, PMID:41344624) mechanism: NAS (UniProt); IMP (FlyBase) verdict: FLAG_FAILS reason: mARC enzymes reduce N-hydroxylated compounds and a fly UGT detoxifies a nitrogenous compound; correct. - go_id: GO:0009956 label: radial pattern formation aspect: BP annotations: - UniProtKB:A0A140LJF1 Nr2f2 (mouse, IMP, PMID:15829524) - UniProtKB:D3YYP4 Nr2f2 (mouse, IMP, PMID:15829524) - UniProtKB:P43135 Nr2f2 (mouse, IMP, PMID:15829524) mechanism: IMP (MGI) verdict: FLAG_FAILS reason: COUP-TFII is required for radial patterning of the mammalian stomach; the term applies to animals. - go_id: GO:0072702 label: response to methyl methanesulfonate aspect: BP annotations: - UniProtKB:P17917 PCNA (fly, IDA, PMID:17087725) - UniProtKB:P17917 PCNA (fly, IEA) - UniProtKB:Q9VIT0 PCNA2 (fly, IDA, PMID:17087725) - UniProtKB:Q9VIT0 PCNA2 (fly, IEA) mechanism: IDA (UniProt); IEA ARBA:ARBA00092661 verdict: FLAG_FAILS reason: PCNA mutants are MMS-sensitive in flies; correct, and the ARBA rows agree. - go_id: GO:0015783 label: GDP-fucose transmembrane transport aspect: BP annotations: - UniProtKB:Q9VHT4 Gfr (fly, IDA, PMID:15530860) - UniProtKB:Q9VHT4 Gfr (fly, IDA, PMID:16344471) - UniProtKB:Q9W429 Efr (fly, IDA, PMID:19948734) mechanism: IDA (FlyBase) verdict: TRUE_BUT_GENERAL reason: Correct; the Gfr and Efr reviews MODIFY these rows to the compartment-specific import terms (Golgi lumen for Gfr, ER lumen for Efr), which each gene already carries. replacement: GO:0036085 GDP-fucose import into Golgi lumen (Gfr); GO:0036084 GDP-fucose import into endoplasmic reticulum lumen (Efr)