agxta notes

Setup and provenance

Fetched with just fetch-gene on Q6DG86 (TrEMBL, 391 aa; synonym agxtl); 7 GOA rows (5 IBA, 2 IEA),
none with a PMID. ZFIN ZDB-GENE-040718-16, Ensembl ENSDARG00000052099, chromosome 6.
The deleted TrEMBL entry F1QY24 (UniParc UPI00015A7661) that PMID:35295584 cites as "Agxta" has a sequence
that differs from Q6DG86 at a single position (checked by fetching UPI00015A7661 from UniParc), so it is the same
gene.
Deep research unavailable: Edison returned 402 Payment Required and the OpenAI key is invalid. Literature
searched by hand via Europe PMC ((agxt OR agxta OR agxtb OR "alanine-glyoxylate aminotransferase") AND zebrafish,
"alanine:glyoxylate aminotransferase" AND (fish OR teleost ...), AGT targeting evolution queries).
DANRE_DUPLICATION batch 4, random draw 11 (seed 20260928); paralog agxtb. PANTHER TGD_tree 1:1 pair
(PTHR21152); Ensembl Compara places the duplication at Osteoglossocephalai.

No experimental study of zebrafish agxta. The only specific statement is from a bioinformatic survey of the
zebrafish peroxisomal proteome:
PMID:35295584
and it contrasts agxtb
PMID:35295584
ZFIN curated expression (Thisse high-throughput in situ, ZDB-PUB-040907-1): liver and pronephric duct from
the 20-25 somite stage to day 5 (bioinformatics output, section 9).

PLP-dependent class-V aminotransferase converting glyoxylate + L-alanine to glycine + pyruvate; also
serine:pyruvate aminotransferase. Deficiency in humans causes primary hyperoxaluria type 1
PMID:12899834.
Organelle distribution varies between species and correlates with diet
PMID:21558762;
PMID:21558762.
Mechanism in mammals: one gene, two start sites. The upstream start adds a cleavable MTS and the downstream
start makes a product that the C-terminal PTS1 sends to peroxisomes
PMID:21558762;
PMID:10723739.
Human AGT is peroxisomal and its KKL PTS1 needs an internal ancillary signal that Xenopus AGT lacks
PMID:15911627.
Mammal-wide study (685 genomes, cell assays) of MTS/PTS1 evolution; Xenopus AGT used as the exclusively
mitochondrial control
PMID:41781394.
Fish biochemistry (species not named in the abstract): hepatic AGT in freshwater fish is in both organelles
PMID:8954944.
Purified mackerel liver AGT has AGT1-type substrate specificity
PMID:6697688.

See agxta-bioinformatics/RESULTS.md. Key points:

agxta starts at the residue equivalent to the mammalian downstream (peroxisomal-form) Met; its 5' UTR and genomic
5' flank have an in-frame stop 16 codons upstream and no in-frame ATG, so no MTS-bearing isoform can be made.
agxta ends SRV; agxtb has a 32-residue Arg-rich N-terminal extension that aligns with the gar extension and ends
SKA. Spotted gar (unduplicated outgroup) has both a 38-residue Arg-rich extension and a C-terminal SKV.
The pattern (a-copies without extension and with S[KR]V/NKM-type ends; b-copies with extension and mostly SKA
ends) recurs across the teleost panel.
Catalytic Lys209 (PLP) and the substrate Arg360 of human AGXT are conserved in both copies.
agxta evolves faster than agxtb relative to gar (59 vs 32 unique changes; chi2 8.01).
Expression overlaps widely (liver, kidney, intestine, spleen, head kidney in Bgee), like gar (liver, mesonephros,
intestine). Larval whole-body TPM: agxtb higher than agxta at day 3-5.

MF (AGT, SPT) IBA/IEA: accepted; catalytic residues conserved.
Peroxisome IBA: accepted; this is the copy that keeps a C-terminal PTS1-like tripeptide and has no MTS.
Glyoxylate catabolism and glycine biosynthesis IBA: accepted (peroxisomal glyoxylate detoxification is the
expected role of the peroxisomal copy), with the caveat that nothing has been measured in zebrafish.