Probable PAINT IRD errors: draft report
Draft for the PANTHER/PAINT curators, generated by paint_report.py. It has not been
sent. Each case links the review that argues it, with verbatim quotes in that file.
1. Family reviews: losses judged contradicted or too broad (14)
| Family | Node | Blocked term | Code | Verdict | Why (from the review) | Suggested | Review |
|---|---|---|---|---|---|---|---|
| PTHR10196 | PTN000023394 | GO:0005829 cytosol | IRD | LOSS_CONTRADICTED | PTN000023394 is the eukaryotic glycerol kinase node (189 leaves: GK/Gk, GK2, GK3P, GK5, Gykl1, Drosophila Gk1/Gk2, yeast GUT1, Arabidopsis GLPK and other plant, fungal and protist glycerol kinases). On the same date (2024-11-19) PAINT placed a mitochondrion IBD on this node and an IRD blocking the cytosol IBD carried by the parent node PTN000023392. | Retract the IRD | interpro/panther/PTHR10196/PTHR10196-review.yaml |
| PTHR10638 | PTN000067358 | GO:0008131 primary methylamine oxidase activity | IRD | LOSS_CONTRADICTED | This IRD NOT sits on the eutherian AOC3 clade (21 leaves; human, mouse and rat AOC3 and their orthologues in PTHR10638:SF23 MEMBRANE PRIMARY AMINE OXIDASE, plus a few unnamed great-ape SF94 sequences) and blocks the GO:0008131 IBD placed at PTN000067313. AOC3 is VAP-1, the semicarbazide-sensitive amine oxidase (SSAO), one of the best-characterised copper amine oxidases. | Retract the IRD | interpro/panther/PTHR10638/PTHR10638-review.yaml |
| PTHR10648 | PTN000068762 | GO:0005829 cytosol | IRD | LOSS_CONTRADICTED | PTN000068762 is a single leaf, Arabidopsis PP2AA3 (Q38951, AT1G13320, SF36). The IRD blocks the cytosol IBD on the eukaryotic PP2A scaffold-subunit node PTN000068663, and both rows carry the same date (2025-09-02). | Retract the IRD | interpro/panther/PTHR10648/PTHR10648-review.yaml |
| PTHR11588 | PTN000172659 | GO:0005874 microtubule | IRD | LOSS_CONTRADICTED | This IRD stops the tubulin-root IBD for microtubule (PTN000172598, seeded by alpha and beta tubulins) from descending into the gamma-tubulin clade (134 leaves; subfamilies SF7, SF62, SF79, SF381). The curator's intent is clear and biologically right in one sense: gamma-tubulin is not a lattice-forming tubulin, and the node instead carries IBDs for gamma-tubulin complex, spindle pole and microtubule nucleator activity. | Retract the IRD | interpro/panther/PTHR11588/PTHR11588-review.yaml |
| PTHR11588 | PTN000172725 | GO:0005737 cytoplasm | IRD | LOSS_CONTRADICTED | This IRD stops the tubulin-root IBD for cytoplasm (PTN000172598) from descending into the Viridiplantae gamma-tubulin clade (62 leaves, all in SF7 TUBULIN GAMMA CHAIN, including Arabidopsis TUBG1 and TUBG2). Animal and fungal gamma-tubulins still inherit the term. | Retract the IRD | interpro/panther/PTHR11588/PTHR11588-review.yaml |
| PTHR11610 | PTN000176957 | GO:0005576 extracellular region | IRD | LOSS_CONTRADICTED | PTN000176957 is the therian PNLIPRP1 orthogroup (nine leaves, all SF108). On 2026-05-28 PAINT placed IRDs here on lipase activity, extracellular region and lipid catabolic process, all overriding PTN008325466. | Retract the IRD | interpro/panther/PTHR11610/PTHR11610-review.yaml |
| PTHR11972 | PTN001379754 | GO:0000293 ferric-chelate reductase activity | IRD | LOSS_CONTRADICTED | The IRD node is a single leaf, Arabidopsis FRO6 (Q8RWS6, At5g49730, subfamily SF69), and it blocks the ferric-chelate reductase IBD placed at the embryophyte node PTN000944413, whose seeds include the tandem paralog FRO7 (At5g49740). FRO6 and FRO7 are 87% identical and differ only in their N termini (FRO7 carries the stronger plastid transit peptide), so a sequence-level loss of catalysis in FRO6 alone is not expected. | Retract the IRD | interpro/panther/PTHR11972/PTHR11972-review.yaml |
| PTHR11972 | PTN002279285 | GO:0016175 superoxide-generating NAD(P)H oxidase activity | IRD | LOSS_TOO_BROAD | In the upstream PANTHER IBD.gaf, the ancestral GO:0016175 IBD at PTN000239644 (dated 20230405) has a single seed, SGD:S000003128, which is S. cerevisiae AIM14/YNO1 (P53109). The IRD at PTN002279285 has the same date and covers a 42-leaf Dikarya clade of FRE-like proteins that contains AIM14 itself (leaf PTN000944297). | Move the IRD to a lower node | interpro/panther/PTHR11972/PTHR11972-review.yaml |
| PTHR19375 | PTN001065099 | GO:0042026 protein refolding | IRD | LOSS_TOO_BROAD | PTN001065099 is not the ribosome-associated branch alone. Its 57 members span all of the fungal cytosolic Hsp70 subfamilies: the SSA chaperones (SF395 with S. cerevisiae SSA1/SSA2, S. pombe ssa1/ssa2, Neurospora hsps-1; SF385 with SSA3/SSA4), the ribosome-associated SSB group (SF467: SSB1/SSB2, S. pombe sks2), the RAC subunit SSZ1 (SF539) and a small LHS1-like group (SF522). | Move the IRD to a lower node | interpro/panther/PTHR19375/PTHR19375-review.yaml |
| PTHR24056 | PTN000756102 | GO:0004674 protein serine/threonine kinase activity | IRD | LOSS_CONTRADICTED | PTN000756102 is the CDKL5 clade (40 leaves, almost all PTHR24056:SF111, plus the zebrafish/medaka SF547 copies): vertebrate CDKL5, amphioxus, sea urchin, Monosiga, budding yeast YGK3, Giardia, Paramecium, Phytophthora, Chlamydomonas and Klebsormidium sequences. The IRD blocks the deep GO:0004674 IBD at PTN000623091 from descending, while the same node keeps an IBA for the parent GO:0004672 protein kinase activity from PTN000623091. | Retract the IRD | interpro/panther/PTHR24056/PTHR24056-review.yaml |
| PTHR24056 | PTN000623095 | GO:0016592 mediator complex | IRD | LOSS_CONTRADICTED | PTN000623095 is the bilaterian CDK8/CDK19 clade (60 leaves): vertebrate CDK8 (SF243) and CDK19 (SF570), plus invertebrate Cdk8 (SF495, e.g. Drosophila Cdk8 and C. elegans cdk-8) and nematode dyf-18 (SF469). | Retract the IRD | interpro/panther/PTHR24056/PTHR24056-review.yaml |
| PTHR42884 | PTN001647685 | GO:0005802 trans-Golgi network | IRD | LOSS_CONTRADICTED | PTN001647685 is the PC1/3 (PCSK1) orthogroup (29 leaves, all SF14). PAINT placed the TGN IBD on the opisthokont node PTN000082856 on 2024-11-21, seeded by furin (mouse MGI:97513, human P09958), yeast KEX2 (SGD:S000005182), rat Pcsk5 (RGD:620326) and rat Pcsk1 (RGD:3272). | Retract the IRD | interpro/panther/PTHR42884/PTHR42884-review.yaml |
| PTHR45618 | PTN000642212 | GO:0017077 oxidative phosphorylation uncoupler activity | IRD | LOSS_CONTRADICTED | This IRD NOT covers the mammalian UCP3 clade (15 leaves, all in PTHR45618:SF2 MITOCHONDRIAL TRANSPORTER UCP3-RELATED, including human, mouse and rat UCP3) and blocks the GO:0017077 IBD at PTN000642156 that PAINT seeded from MGI:98894, RGD:3931 and Arabidopsis AT3G54110. GO:0017077 is defined as proton transfer into the matrix that dissipates the gradient (proton leak); it does not require thermogenesis. | Retract the IRD | interpro/panther/PTHR45618/PTHR45618-review.yaml |
| PTHR45807 | PTN002910252 | GO:0007259 cell surface receptor signaling pathway via JAK-STAT | IRD | LOSS_CONTRADICTED | This row is a negated IRD (dated 2026-08-28, the same day the Bilateria GO:0007259 IBD was refreshed). It asserts that the euteleostome TYK2 clade (SF6) has diverged so far that it no longer takes part in receptor JAK-STAT signaling, and its effect is that human and mouse TYK2 get no GO:0007259 IBA (confirmed in QuickGO). | Retract the IRD | interpro/panther/PTHR45807/PTHR45807-review.yaml |
2. Gene reviews: losses judged contradicted or too broad (4)
From propagation_review.paint_losses in the gene reviews, for losses no family
review has assessed. The quoted evidence is in each gene review.
| Family | Node | Blocked term | Code | Clade (leaves) | Judged | Gene (row) | Why (from the review) | Suggested | Review |
|---|---|---|---|---|---|---|---|---|---|
| PTHR13194 | PTN000995776 | GO:0010257 NADH dehydrogenase complex assembly | IRD | 11 | CONTRADICTED | cia30 (IBA:ACCEPT) | N. crassa cia30 disruption mutants accumulate the matrix arm and the small membrane-arm intermediate but cannot form the large membrane-arm assembly intermediate of complex I (PMID:9769214). The IRD clade is fungal CIA30/NDUFAF1 (11 proteins, including N. crassa cia30) and includes complex I-containing fungi. | Retract the IRD, or restrict it to a branch that has lost complex I. | genes/NEUCR/cia30/cia30-ai-review.yaml |
| PTHR10454 | PTN000047958 | GO:0031265 CD95 death-inducing signaling complex | IRD | 6 | CONTRADICTED | CFLAR (IBA:ACCEPT) | The CD95/TRAILR-FADD DISC assembles with procaspase-8 and cFLIP (PMID:38710704). The IRD clade is mammalian CFLAR (6 proteins). The other CFLAR IRDs on this node (endopeptidase activity, macrophage differentiation, neuron apoptosis) agree with the gene review. | Retract the IRD for GO:0031265 only. | genes/human/CFLAR/CFLAR-ai-review.yaml |
| PTHR12929 | PTN000309189 | GO:0032217 riboflavin transmembrane transporter activity | IRD | 4 | CONTRADICTED | SLC52A1 (IBA:ACCEPT) | Human SLC52A1 (RFVT1) transports riboflavin in direct assays (IDA, PMID:20463145 and PMID:21854757). The IRD node is the primate SLC52A1 clade (4 proteins), and it blocks both GO:0032217 riboflavin transmembrane transporter activity and GO:0032218 riboflavin transport. | Retract the IRD for GO:0032217 and GO:0032218. | genes/human/SLC52A1/SLC52A1-ai-review.yaml |
| PTHR12929 | PTN000309189 | GO:0032218 riboflavin transport | IRD | 4 | CONTRADICTED | SLC52A1 (IBA:ACCEPT) | Human SLC52A1 (RFVT1) transports riboflavin in direct assays (IDA, PMID:20463145 and PMID:21854757). The IRD node is the primate SLC52A1 clade (4 proteins), and it blocks both GO:0032217 riboflavin transmembrane transporter activity and GO:0032218 riboflavin transport. | Retract the IRD for GO:0032217 and GO:0032218. | genes/human/SLC52A1/SLC52A1-ai-review.yaml |
3. Stale overrides: the blocked IBD is gone (14)
The IRD's ancestral node no longer carries an IBD for the term, so the IRD blocks
nothing and could be removed. Source: PAINT IBD.gaf via fetch_paint_ird.py.
| Family | IRD node | Term | Ancestral node | IRD date |
|---|---|---|---|---|
| PTHR11802 | PTN001720128 | GO:0005773 vacuole | PTN001720040 | 20210904 |
| PTHR12260 | PTN000262554 | GO:0005634 nucleus | PTN000262496 | 20240305 |
| PTHR12897 | PTN000984912 | GO:0005765 lysosomal membrane | PTN000307264 | 20240306 |
| PTHR12919 | PTN002293408 | GO:0032543 mitochondrial translation | PTN000308745 | 20240306 |
| PTHR13681 | PTN002299200 | GO:0000381 regulation of alternative mRNA splicing, via spliceosome | PTN001784834 | 20250826 |
| PTHR24261 | PTN001546628 | GO:0031012 extracellular matrix | PTN002799862 | 20250903 |
| PTHR33269 | PTN002115829 | GO:0045271 respiratory chain complex I | PTN004990314 | 20240801 |
| PTHR43048 | PTN000482983 | GO:0005739 mitochondrion | PTN001468099 | 20241121 |
| PTHR43782 | PTN002886720 | GO:0005634 nucleus | PTN000144387 | 20200401 |
| PTHR43795 | PTN008453022 | GO:0009507 chloroplast | PTN008453015 | 20260710 |
| PTHR45639 | PTN009180209 | GO:0030968 endoplasmic reticulum unfolded protein response | PTN000452651 | 20260224 |
| PTHR45688 | PTN000241152 | GO:0005739 mitochondrion | PTN000241036 | 20240229 |
| PTHR45688 | PTN000241488 | GO:0005739 mitochondrion | PTN000241036 | 20240229 |
| PTHR46590 | PTN008709838 | GO:0005739 mitochondrion | PTN008709837 | 20250904 |
4. Fully re-annotated: the IRD blocks nothing (20)
Every protein in the clade still gets a more specific term (is_a or part_of below the
blocked one) as a positive IBA, from the IRD node itself or an ancestor. The IRD then
contradicts PAINT's own propagation: it should also block that term, or be retracted.
Source: ird_seed_check.py (see ird_seed_check.md).
| Family | IRD node | Blocked term | IRD date | Clade (checked/all) | Kind | IBA sources (node, term, where) |
|---|---|---|---|---|---|---|
| PTHR10131 | PTN007421972 | GO:0007166 cell surface receptor signaling pathway | 20250411 | 3/3 | above | PTN000805720 GO:0033209 (above) |
| PTHR10794 | PTN000082718 | GO:0034338 short-chain carboxylesterase activity | 20200313 | 1/1 | above | PTN000082647 GO:0008126 (above) |
| PTHR11119 | PTN002476593 | GO:0015882 L-ascorbic acid transmembrane transport | 20241120 | 1/1 | above | PTN002595861 GO:0015229 (above) |
| PTHR11610 | PTN000176957 | GO:0016042 lipid catabolic process | 20241120 | 9/9 | above | PTN000906454 GO:0019433 (above) |
| PTHR11610 | PTN000176957 | GO:0016298 lipase activity | 20260528 | 9/9 | above | PTN000906454 GO:0004465 (above); PTN000906454 GO:0008970 (above) |
| PTHR11610 | PTN008325477 | GO:0016042 lipid catabolic process | 20241120 | 12/12 | above | PTN000906454 GO:0019433 (above) |
| PTHR11610 | PTN008325477 | GO:0016298 lipase activity | 20260528 | 12/12 | above | PTN000906454 GO:0004465 (above); PTN000906454 GO:0008970 (above) |
| PTHR11958 | PTN002632768 | GO:0015813 L-glutamate transmembrane transport | 20250903 | 20/20 | above | PTN000238242 GO:0005313 (above) |
| PTHR19321 | PTN004511774 | GO:0005819 spindle | 20230603 | 1/1 | above | PTN000448590 GO:1990023 (above) |
| PTHR24056 | PTN000623365 | GO:0000307 cyclin-dependent protein kinase holoenzyme complex | 20260313 | 1/1 | above | PTN000623095 GO:1990508 (above) |
| PTHR24221 | PTN000657226 | GO:0055085 transmembrane transport | 20250903 | 10/10 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN000657241 | GO:0055085 transmembrane transport | 20250903 | 12/12 | same node | PTN000657189 GO:0042626 (above); PTN000657241 GO:0042910 (same node) |
| PTHR24221 | PTN000657258 | GO:0055085 transmembrane transport | 20250903 | 1/1 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN000657261 | GO:0055085 transmembrane transport | 20250903 | 1/1 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN001542468 | GO:0055085 transmembrane transport | 20250903 | 3/3 | above | PTN000657189 GO:0042626 (above) |
| PTHR24235 | PTN000662954 | GO:0007218 neuropeptide signaling pathway | 20250618 | 8/8 | above | PTN002538187 GO:0008188 (above) |
| PTHR33694 | PTN008658623 | GO:0005737 cytoplasm | 20260828 | 54/54 | same node | PTN008658623 GO:0005739 (same node) |
| PTHR43020 | PTN000228777 | GO:0035596 methylthiotransferase activity | 20260530 | 85/85 | above | PTN000228824 GO:0035597 (above) |
| PTHR43020 | PTN000228777 | GO:0035600 tRNA methylthiolation | 20241121 | 85/85 | above | PTN000228824 GO:0035597 (above) |
| PTHR48017 | PTN004585555 | GO:0003333 amino acid transmembrane transport | 20260828 | 31/31 | above | PTN001118955 GO:0015171 (above) |