Q9VQ04 is the single 240-residue CG5565-PA product in the current FlyBase record. The complete HAD-family architecture is compatible with the manually transferred PUDP activity; it is not a truncated native isoform.
PMID:20722631(https://pubmed.ncbi.nlm.nih.gov/20722631/) characterized human HDHD1/PUDP Q08623: purified enzyme hydrolyzed pseudouridine 5′-phosphate with Km 0.3 μM and at least 1000-fold greater catalytic efficiency than the other tested phosphate esters. GOA specifically records manual ortholog transfer from that experimentally characterized protein. The proposed core function is a qualified inference rather than a direct fly assay.
The ProtNLM structural donor Q9V1B3 is a Pyrococcus protein; its glyceraldehyde-3-phosphate statement is itself by similarity to Q58832. Shared structure does not determine substrate specificity. Conversely the existence of a better-supported physiological substrate cannot refute the explicitly in vitro side-activity claim, which remains UNC. The source is a function paragraph only, with no original GO predictions.
The Falcon report was inspected. Its discussion of HAD substrate ambiguity is relevant, but its “no specific reaction without biochemical testing” recommendation misses the current FlyBase PUDP ortholog transfer to experimentally characterized human Q08623. A full-length comparison with that human protein retains both catalytic Asp positions and covers 226 of 228 human residues; the original archaeal structural donor is substantially less similar in sequence. This supports accepting the qualified PUDP transfer while keeping the separate in vitro substrate claim unresolved. The comparison alone does not establish orthology or prove a particular substrate. Inputs, script, alignments, controls and RESULTS.md are retained.