DPH3P1

Summary: Inherited from the DPH3 ortholog node, which is seeded by yeast Dph3/Kti11 iron binding. The DPH3P1 sequence keeps all four metal-ligand cysteines, but the locus is a processed pseudogene with no evidence of transcription into mRNA or of translation.

Reason: The PAINT inference at PTN000485452 is sound for genuine DPH3 orthologs. Yeast Dph3 binds iron through four conserved cysteines (PMID:24422557). DPH3P1 is a leaf in that clade only because it is a recent processed retrocopy of DPH3. Its residues do not argue against the inference: the conceptual translation keeps C26, C28, C48 and C51 (file:human/DPH3P1/DPH3P1-bioinformatics/RESULTS.md). The annotation fails at the first Tier 3 question instead, because the product is not shown to exist. HGNC classifies the locus as a pseudogene, Ensembl annotates a processed_pseudogene transcript with no translation, GTEx reports no expression, and UniProt rates it PE 5 with a pseudogene caution. Marked as over-annotated rather than removed, under the Tier 3 rule used across this project. A binding activity whose residue basis is intact is not contradicted by the sequence, and the doubt is only about whether a product is made. Terms that need more than the intact site (the diphthamide process and cytosol rows) are removed.

Summary: Cytosolic location inherited from DPH3 orthologs. It is correct for DPH3, but there is no evidence that a DPH3P1 protein is made.

Reason: Cytosolic DPH3 is consistent with its partners: Cbr1 reduces the cytosolic Dph3 (PMID:27694803), and the node placement is reasonable for real DPH3 orthologs. DPH3P1 is a processed pseudogene. HGNC classifies it as a pseudogene, Ensembl has no translated transcript, GTEx shows no expression and UniProt rates it PE 5. A location cannot be assigned to a product that is not shown to exist.

Summary: Diphthamide biosynthesis role inherited from DPH3 orthologs. DPH3 does the work as the electron donor to Dph1-Dph2, but this pseudogene locus has no evidence of a product.

Reason: Yeast Dph3 reduces the Dph1-Dph2 Fe-S cluster in the first step of diphthamide biosynthesis (PMID:24422557) and donates an iron atom to form the [4Fe-4S] cluster (PMID:34154323), so DPH3 orthologs do participate in this process. For DPH3P1 the phylogenetic inference is not undermined by residue loss, because the metal ligands are retained. The locus is a processed pseudogene with no evidence of transcription into mRNA or of translation, and no study has asked whether a DPH3P1 product could substitute for DPH3 in eEF2 diphthamide modification. Human cells depend on DPH3 for this process.

Summary: InterPro2GO mapping from the DPH3/4-like family (IPR044248) to diphthamide modification, applied to a conceptual translation of a processed pseudogene.

Reason: The domain match is real, because the sequence is a near copy of DPH3. However, the locus is a processed pseudogene with no coding transcript, no expression in GTEx and PE 5 protein existence. The same reasoning as for the IBA row applies. Family membership of a hypothetical translation does not establish that a gene product takes part in diphthamide biosynthesis.

Summary: Generic metal ion binding from the DPH3/4-like InterPro family. The cysteine ligands are present in the conceptual sequence, but there is no evidence the protein exists.

Reason: A translated DPH3P1 sequence would probably bind metal, since C26, C28, C48 and C51 are intact. The annotation is still a function claim for a product of a processed pseudogene that is not shown to be transcribed into mRNA or translated. As with the iron ion binding IBA, the doubt rests on the locus status and not on residue loss, so the row is marked as over-annotated rather than removed (the Tier 3 rule for residue-intact activities on products of doubtful existence).