Date: 2026-10-21. Independent of any ProtNLM2 output.
1. PANTHER placement (PANTHER 19)
Source: PANTHER geneinfo and treeinfo services
(https://www.pantherdb.org/services/oai/pantherdb/geneinfo?geneInputList=Q7SAD4&organism=367110,
https://www.pantherdb.org/services/oai/pantherdb/treeinfo?family=PTHR23023), queried 2026-10-21.
Q7SAD4 is placed in PTHR23023:SF292 FLAVIN-BINDING MONOOXYGENASE-LIKE PROTEIN (AFU_ORTHOLOGUE AFUA_6G01900).
Path from the leaf to the root of the PTHR23023 tree (reproduced by panther_placement.py, output panther_placement_output.txt):
| node |
event |
taxon |
subfamily |
leaves |
| PTN000545913 |
duplication |
(Neurospora in-paralogs) |
SF292 |
2 (NCU06296, NCU08749) |
| PTN001125012 |
speciation |
Sordariomyceta |
SF292 |
4 |
| PTN001125011 |
speciation |
Sordariomycetes-Leotiomycetes |
SF292 |
5 |
| PTN002744969 |
duplication |
Sordariomycetes-Leotiomycetes |
SF292 |
8 |
| PTN002346104 |
speciation |
Pezizomycotina |
SF292 |
11 (incl. Aspergillus fumigatus AFUA_6G01900, A. nidulans ANIA_02629/ANIA_08660) |
| PTN008587727 |
duplication |
Pezizomycotina |
SF226 |
13 |
| PTN008378500 |
speciation |
Dikarya |
SF226 |
15 |
| PTN007724818 |
speciation |
Fungi |
SF226 |
16 |
| PTN000545687 |
speciation |
Opisthokonts |
SF226 |
215 (sister to the whole animal FMO clade) |
| PTN008378499 |
speciation |
Eukaryota |
SF226 |
497 (adds plant FMOs) |
| PTN004593253 |
duplication |
Eukaryota |
SF266 |
842 |
| PTN000545685 |
speciation |
LUCA |
SF266 |
848 |
| PTN009058586 |
root |
- |
- |
850 |
Findings:
- The fungal clade containing Q7SAD4 is joined to the animal FMO clade by a speciation node
(Opisthokonts). Human FMO1, FMO2, FMO3, FMO4 and FMO5 arise from later animal duplications
and are therefore all co-orthologs of the fungal clade at equal phylogenetic distance; each
sits in its own subfamily (SF154, SF84, SF44, SF74, SF78), not in SF292.
- No member of SF292 or of the fungal clade has experimental GO annotation; every leaf in the
Fungi node is an uncharacterised genome-project entry.
- The IBA "monooxygenase activity" on Q7SAD4 lists PANTHER:PTN009058586, the family root.
The PANTHER GO-slim MF annotation on every node of the path carries only generic terms
(oxidoreductase, monooxygenase, NAD(P)H-dependent single-oxygen-incorporating oxidoreductase
GO:0016709); no substrate-specific activity (e.g. GO:0004499) is placed on any ancestor.
- Yeast FMO1 (P38866, the yFMO of PMID:10077572) is classified by PANTHER 19 in a different
family, PTHR43539:SF78; S. pombe fmo1 (Q9HFE4) is in PTHR23023:SF266 on a branch outside the
Eukaryota SF226 clade. Neither is a close relative of Q7SAD4.
2. Motif and hydrophobicity scan
Scripts: motif_scan.py (output motif_scan_output.txt) and align_fmo3.py
(output align_fmo3_output.txt), run with uv run --script.
- FAD-binding Rossmann motif GxGxxG is conserved at residues 10-15 (GSGLFG), aligned to
FMO3 GAGVSG (9-14).
- The FMO-identifying motif FxGxxxHxxxY of FMO3 (FKGKCFHSRDY, 166-176) is not present as a
contiguous motif; the global alignment maps it to Q7SAD4 159-175 with an insertion, and the
aligned residues read FKGQ...LFHSKEL (F, K, G and the H-S pair retained).
- The second (NADPH-binding) GxGxxG motif of FMO3 (GLGNSG, 191-196) is not conserved; the
aligned Q7SAD4 segment (191-209, VLGSKG in the alignment, around VVTVLGGTKSAWD) lacks the
GxGxxG pattern.
- The FMO3 FATGY motif (327-331) has no aligned counterpart in Q7SAD4.
- Global identity to FMO3 over 441 aligned pairs is 29.3%.
- No 19-residue Kyte-Doolittle window reaches 1.6 in Q7SAD4 (mammalian FMO3 has a C-terminal
membrane anchor that does reach this threshold); the Q7SAD4 C-terminus is charged.
Interpretation (inconclusive on cofactor specificity): the FAD-binding motif and the core of
the FMO motif are retained, consistent with a flavin-dependent monooxygenase. The canonical
NADPH-binding dinucleotide motif and FATGY are diverged, so NADPH (versus NADH) preference
cannot be read from the sequence. There is no predicted C-terminal membrane anchor of the
mammalian type, so ER-membrane localization of mammalian FMOs should not be transferred.