PHOSPHORYLATION_REFACTOR cross-species re-audit

Species: DROME, DANRE, ARATH, rat

Warnings (25)

Cross-Species Re-Audit

2026-09-28

This re-audit revisits the fly, zebrafish, Arabidopsis and rat query-level
findings that were added on 2026-01-19. Those sections predated full
GENE-ai-review.yaml curation for these species, and the original query
counted at least one NOT annotation as though it were a positive assertion.
The dated current-goa-2026-09-28.tsv
sidecar records total fetched GOA rows, positive protein-phosphorylation rows,
negated protein-phosphorylation rows and the related GOA rows used to make the
calls below.

Rules used here:

The main project counts should therefore treat fly/ZFIN/TAIR/RGD as a
row-level triage, not as completed gene reviews.

FlyBase

Gene Current GOA row Current call Rationale
DROME/Mulk No positive protein-phosphorylation BP row; IDA GO:0046834 lipid phosphorylation from PMID:22069480 False positive Mulk currently carries ceramide/acylglycerol kinase molecular functions and a lipid-phosphorylation process row. That is not a protein-phosphorylation error.
DROME/rdgA No positive protein-phosphorylation BP row; TAS GO:0046834 lipid phosphorylation from PMID:11707492 False positive rdgA is a diacylglycerol kinase. The only phosphorylation process hit in current GOA is lipid phosphorylation.
DROME/Argk1 No positive protein-phosphorylation BP row Stale hit Current GOA has arginine kinase molecular-function rows, but no GO:0006468 or GO:0046777 biological-process row.
DROME/Dref ISS GO:0006468 protein phosphorylation and GO:0046777 protein autophosphorylation from GO_REF:0000024, WITH/FROM human CAMKK2 Remove Dref is a BED-domain transcription factor rather than a kinase; the positive protein-phosphorylation rows are old ISS transfers from human CAMKK2, not a FlyBase or PAINT assertion.
DROME/CG9886 (Glyctk) ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human GLYCTK Remove CG9886 is glycerate kinase, EC 2.7.1.31, and current GOA already has GO:0008887 glycerate kinase activity. The propagated human GLYCTK GO:0006468 row is the same wrong-substrate error seen in mammals.

Zebrafish

Gene Current GOA row Current call Rationale
DANRE/glyctk ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human GLYCTK Remove Zebrafish glyctk is glycerate kinase, EC 2.7.1.31, and current GOA already has GO:0008887 glycerate kinase activity. The protein-phosphorylation row should not have propagated from human GLYCTK.

Arabidopsis

Gene Current GOA row Current call Rationale
ARATH/CRY2 Negated GO:0016301 kinase activity and GO:0046777 protein autophosphorylation, both PMID:17073458 False positive This is the important qualifier bug: the rows are negated and are already accepted in genes/ARATH/CRY2/CRY2-ai-review.yaml. They should never be counted as incorrect positive phosphorylation annotations.
ARATH/TOPP4 IPI GO:0006468 protein phosphorylation from PMID:26704640, with PIF5 Remove TOPP4 is a type 1 protein phosphatase. The cited abstract says TOPP4 interacts with PIF5 and dephosphorylates it, so the gene acts on the opposite side of the phosphorylation cycle.
ARATH/CDC25 IDA GO:0006468 protein phosphorylation from PMID:15336525 Remove PMID:15336525 characterizes Arath;CDC25 as a dual-specificity tyrosine phosphatase, and current GOA also has GO:0004725 protein tyrosine phosphatase activity.
ARATH/PWD No positive protein-phosphorylation BP row Stale hit Current fetched GOA no longer has a protein autophosphorylation row for PWD.
ARATH/CKB2 No positive protein-phosphorylation BP row Stale hit Current fetched GOA no longer has a protein-phosphorylation row for the CK2 beta regulatory subunit.
ARATH/RIN4 IDA GO:0006468 protein phosphorylation from PMID:11955429 Remove RIN4 is the immune regulator whose phosphorylation is induced by AvrRpm1 and AvrB; the cached abstract describes phosphorylation of RIN4, not phosphorylation by RIN4.
ARATH/ATPI4K_ALPHA (PI4KA1) IDA GO:0006468 protein phosphorylation from PMID:9712908 Modify to GO:0046834 lipid phosphorylation PI4KA1 is phosphatidylinositol 4-kinase alpha 1, EC 2.7.1.67. The PMID:9712908-linked evidence supports PI4K activity and phosphoinositide binding, not phosphorylation of protein substrates.
ARATH/PI4KG7 IDA GO:0046777 protein autophosphorylation from PMID:17880284 Keep This was mislabeled as a lipid-kinase error in January. The PMID:17880284 abstract says AtPI4Kgamma7 undergoes autophosphorylation and phosphorylates Ser/Thr protein substrates.
ARATH/AAK1 (FER) IDA GO:0046777 protein autophosphorylation from PMID:17673660 Keep AAK1 resolves to FERONIA, a receptor-like protein kinase; the same PMID also supports an IDA GO:0004672 protein kinase activity row in current GOA.
ARATH/LecRK-I.5 IDA GO:0006468 protein phosphorylation from PMID:32345768 Keep P2K2/LecRK-I.5 is a receptor-like protein kinase, and the PMID:32345768 abstract says P2K2 and P2K1 cross-phosphorylate after extracellular ATP treatment.
ARATH/LecRK-I.8 IDA GO:0046777 protein autophosphorylation from PMID:28722654 Keep The full text of PMID:28722654 reports "strong autophosphorylation activity" by the LecRK-I.8 kinase domain.

Rat

Gene Current GOA row Current call Rationale
rat/Gas6 ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human GAS6 Modify to GO:0045860 positive regulation of protein kinase activity This is the same TAM-receptor ligand pattern as mouse Gas6. The ligand activates receptor tyrosine kinases and downstream ERK/PI3K signaling; it does not catalyze the phosphorylation reaction.
rat/Glyctk ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human GLYCTK Remove Glyctk is a small-molecule glycerate kinase, and current GOA already has multiple GO:0008887 glycerate kinase activity rows.
rat/Ilf3 ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM mouse Ilf3 Remove Human ILF3 has the corresponding IDA row reviewed as a substrate error: ILF3/NFAR is phosphorylated by PKR rather than being a kinase.
rat/Pdgfb ISS GO:0006468 protein phosphorylation and GO:0018108 peptidyl-tyrosine phosphorylation from GO_REF:0000024, WITH/FROM human PDGFB Modify to GO:0048008 platelet-derived growth factor receptor signaling pathway These mirror the human PDGFB rows; PDGFB is the secreted ligand, not the receptor tyrosine kinase.
rat/Prrt1 ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM mouse Prrt1 Remove The human PRRT1 review rejected this same assertion: PRRT1/SynDIG4 affects basal GRIA1 phosphorylation indirectly as an AMPAR auxiliary subunit and has no kinase domain.
rat/Ywhaz ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human YWHAZ Modify to GO:0045859 regulation of protein kinase activity The human YWHAZ review recasts this as regulation of phosphorylation. 14-3-3 zeta binds phosphoserine clients and modulates kinase pathways but is not itself the kinase.
rat/Ppp3cb ISS GO:0006468 protein phosphorylation from GO_REF:0000024, WITH/FROM human PPP3CB Remove Ppp3cb is the calcineurin catalytic subunit, a calcium/calmodulin-dependent protein phosphatase. The positive protein-phosphorylation row is the opposite reaction.
rat/Grm5 IDA GO:0006468 protein phosphorylation from PMID:15758184 Remove PMID:15758184 supports mGluR5-dependent ERK1/2 phosphorylation through Homer1b/c. The same current GOA file already has GO:0043410 positive regulation of MAPK cascade for this reference.
rat/Pick1 IDA GO:0006468 protein phosphorylation from PMID:11237868 Modify to GO:0045859 regulation of protein kinase activity The PMID:11237868 abstract says rPICK1 modulates PKC phosphorylation of TIS21 through binding; PICK1 is the PDZ scaffold, not PKC.
rat/Thy1 IDA GO:0046777 protein autophosphorylation from PMID:19723805 Remove Thy-1 is a GPI-anchored ligand. The full text says "FAK autophosphorylation on Y397 is triggered by Thy-1" downstream of integrin and syndecan-4 engagement in astrocytes.