Gene Ontology annotation through association of InterPro records with GO terms
TreeGrafter-generated GO annotations
Combined Automated Annotation using Multiple IEA Methods
UniProtKB entry Q88HG4 for Pseudomonas putida KT2440 PP_3394
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The fetched UniProt record contains an alpha-isopropylmalate/homocitrate-synthase signature, in conflict with its electronic HMG-CoA lyase assignment.
"InterPro; IPR002034; AIPM/Hcit_synth_CS."
The Pseudomonas aeruginosa liuE gene encodes the 3-hydroxy-3-methylglutaryl coenzyme A lyase, involved in leucine and acyclic terpene catabolism.
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Biochemical characterization of P. aeruginosa LiuE provides the positive HMG-CoA lyase comparator against which the conflicting PP_3394 signatures were evaluated.
"cleavage of HMG-CoA to acetyl-CoA and acetoacetate."
OpenScientist gene research for PSEPK mvaB
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The provider reports that MvaB is much closer to characterized P. aeruginosa LiuE than it is to PP_3394.
"| mvaB (PP_3540) vs. *P. aeruginosa* LiuE/PA2011 (characterized HMG-CoA lyase) | **78.6%** |"
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The provider reports moderate identity between the two KT2440 paralogs; it does not report a direct PP_3394-to-LiuE comparison.
"| mvaB vs. KT2440 paralog PP_3394 | 41.8% |"
OpenScientist focused report on PP_3394 DRE-TIM reaction and pathway specificity
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MvaB/PP_3540, not PP_3394, is the best supported leucine/terpene HMG-CoA lyase in P. putida KT2440.
"the leucine/terpene HMG-CoA-lyase function of *P. putida* belongs to **mvaB / PP_3540**"
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PP_3394 fails the HMG-CoA-lyase-specific active-site signature used to distinguish the canonical lyases from related DRE-TIM synthases.
"PP_3394 FAILS the HMG-CoA-lyase-specific PROSITE active-site signature PS01062 (SVAGLGGCPY)"
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PP_3394 should be treated as a catalytically competent DRE-TIM metallolyase of unresolved substrate specificity.
"divergent DRE-TIM metallolyase, specificity undetermined by sequence"
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The PP_3394-specific discriminators are computational; direct biochemistry or a mutant phenotype is still absent.
"All of the discriminating evidence is *computational* (pairwise alignment, PROSITE/motif scanning, and a whole-sequence NJ phylogeny). There is **no direct biochemical assay or mutant phenotype for PP_3394 itself**"
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The bacterial PP_3394 annotation should not carry a mammalian ketone-body biosynthesis process term.
""Ketone-body biosynthesis" is a mammalian physiological concept and should not be transferred to this bacterium regardless of enzyme family."
Cached OpenScientist BCAA-catabolism module report for Pseudomonas putida KT2440
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The generated module report explicitly leaves PP_3394 versus MvaB unresolved as the displaced HMG-CoA lyase candidate.
"Both are candidates for the displaced leucine terminal step; choice is **unresolved** and should be flagged."