Gene Ontology annotation through association of InterPro records with GO terms
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
TreeGrafter-generated GO annotations
Combined Automated Annotation using Multiple IEA Methods
UniProtKB entry for PP_1969
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UniProt identifies Q88LG4 as a MoaA-like radical-SAM protein.
"DR InterPro; IPR006638; Elp3/MiaA/NifB-like_rSAM.
DR InterPro; IPR040064; MoaA-like."
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UniProt assigns a [4Fe-4S] cofactor by automated rule.
"CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|ARBA:ARBA00001966};"
QuickGO GOA annotations for PP_1969
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The fetched table contains adjacent TreeGrafter rows for both exact MoaA and MoaC activities.
"UniProtKB Q88LG4 PP_1969 enables GO:0061798 GTP 3',8'-cyclase activity molecular_function ECO:0007826 IEA GO_REF:0000118 PANTHER:PTN008586333 160488 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) TreeGrafter Radical SAM core domain-containing protein 20260706
UniProtKB Q88LG4 PP_1969 enables GO:0061799 cyclic pyranopterin monophosphate synthase activity molecular_function ECO:0007826 IEA GO_REF:0000118 PANTHER:PTN008586333 160488 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) TreeGrafter Radical SAM core domain-containing protein 20260706"
OpenScientist gene research for PP_1969
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The report incorrectly promotes Q88LG4 from a divergent MoaA-like candidate to canonical MoaA with an exact catalytic assignment.
"PP_1969 encodes **MoaA**, a cytoplasmic **radical S‑adenosyl‑L‑methionine (radical SAM) metalloenzyme** that catalyzes the **first committed step of molybdenum cofactor (Moco) biosynthesis**."
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The report contains concrete locus errors for PP_1294 and PP_3457.
"**moaC = PP_1292, moaD = PP_1293, moaB = PP_1294**, with **moeA = PP_2123** and **mogA = PP_3457**"
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The report presents residue-level motif analysis that was not saved as a reproducible local analysis.
"- N‑terminal radical‑SAM **CX₃CX₂C** motif: **C36**‑N‑Y‑A‑**C40**‑T‑Y‑**C43**."
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The report does acknowledge the absence of direct PP_1969-specific biochemical evidence.
"- **Direct experimental evidence** (crystallography, ENDOR/EPR spectroscopy, in‑vitro reconstitution, mutagenesis) exists for the **MoaA family prototype** (from *Staphylococcus aureus*/*E. coli* systems) and the human ortholog MOCS1A — not specifically for the *P. putida* PP_1969 protein."
Reproducible sequence comparison of KT2440 MoaA-family and MobA-like proteins
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Q88LG4 lacks the two MoaA-specific InterPro records found on Q88E69.
"- The reviewed MoaA sequence Q88E69 is the only one of the three with the
MoaA-specific InterPro entries IPR013483 and IPR000385 in its UniProt record.
All three share broader MoaA-like/radical-SAM entries and PTHR22960."
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The saved report considered shared KEGG K03639 assignment as non-decisive context.
"- The generated KEGG link table maps all three MoaA-family proteins to K03639.
This similarity-driven KO co-assignment is useful context but does not override
the MoaA-specific InterPro split or the low pairwise identities between Q88E69
and the two unreviewed paralogs."
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Q88LG4 is 37.85% identical to canonical Q88E69 and is closer to Q88K11.
"- Q88E69 is 36.25% identical to Q88K11 (PP_2482) and 37.85% identical to Q88LG4
(PP_1969) over aligned residue pairs. Q88K11 and Q88LG4 are 66.15% identical
to one another. This pattern supports a closer relationship between the two
unreviewed candidates than either has to canonical moaA, and does not support
assuming that all three are interchangeable copies."
KEGG gene-to-orthology links for KT2440 MoaA-family proteins
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The reproducible KEGG lookup maps PP_1969 to K03639, the same KEGG orthology as canonical KT2440 MoaA.
"PP_1969 Q88LG4 ppu:PP_1969 ko:K03639"
UniProtKB entry for canonical KT2440 moaA
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Canonical KT2440 MoaA is specifically named as GTP 3',8'-cyclase.
"DE RecName: Full=GTP 3',8-cyclase {ECO:0000255|HAMAP-Rule:MF_01225};"
UniProtKB entry for KT2440 moaC
OpenScientist TreeGrafter stress test of PP_1969 GTP 3',8'-cyclase activity
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The run judges GO:0061798 supported, at the right granularity, with no failure mode applying.
"**Verdict: SUPPORTED.** PP_1969 (UniProt Q88LG4, *Pseudomonas putida* KT2440) is a"
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The run reports both [4Fe-4S]-cluster cysteine triads intact.
"2. **Pseudo-enzyme — PASS.** All six catalytic cysteines of **both** [4Fe-4S]"
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The run states the call is computational, without a P. putida assay.
"- **No direct PSEPK assay:** The function is inferred from orthology + residue"
Ligand-binding residue conservation in KT2440 MoaA paralogs
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All annotated GTP-, SAM- and cluster-binding residues of reviewed KT2440 MoaA are conserved in PP_1969 and PP_2482.
"The divergence of PP_1969 and PP_2482 from canonical KT2440 MoaA does not touch the annotated GTP-, SAM- or cluster-binding residues."
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The PROSITE PS01305 failure reflects substitutions at non-ligand positions.
"The failure of the signature therefore reflects substitutions at non-ligand positions inside an intact CxxxCxxC motif."
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PP_1969 and PP_2482 fall below the TIGR02666 noise and trusted cutoffs, about 100 bits below every reviewed MoaA tested.
"Both paralogs score just below the noise cutoff and about 15-16 bits below the trusted cutoff."
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Both paralogs fail the HAMAP MF_01225_B level-0 cutoff while meeting all of the rule's FT conditions.
"So the HAMAP non-match is a profile-score failure only."
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The model-score loss is spread along the protein, not at annotated ligand positions or in one missing segment.
"The TIGR02666 and MF_01225 non-matches are not explained by a missing non-catalytic segment."
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PP_1969 has no molybdenum-cofactor or molybdoenzyme gene within six loci.
"PP_1969: no molybdenum-cofactor or molybdoenzyme gene in the window"