Gene Ontology annotation through association of InterPro records with GO terms

Genetic and functional characterization of a novel meta-pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1.

The fde meta-pathway continues after A-ring cleavage through steps that yield oxaloacetate.

"After meta-cleavage of the A-ring, the subsequent metabolic steps generate oxaloacetic acid that is metabolized via the tricarboxylic acid cycle."

file:HERSS/Hsero_1011/Hsero_1011-uniprot.txt

UniProtKB entry D8J0X3 for Herbaspirillum seropedicae SmR1 Hsero_1011

The protein has N-terminal and C-terminal fumarylacetoacetase-like domains.

"InterPro; IPR011234; Fumarylacetoacetase-like_C."

file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md

KEGG orthology and reaction assignments for the H. seropedicae fde locus

KEGG assigns Hsero_1011 to FdeI (K26185), linked to R13078 (decarboxylation) and R13079 (unclear dehydration).

"KEGG mapping: `hse:Hsero_1011 -> ko:K26185` (fdeI; naringenin degradation protein FdeI)"

file:PSEPK/PP_3205/PP_3205-bioinformatics/RESULTS.md

Reproducible PP_3205 and Hsero_1011 sequence and KEGG comparison

The P. putida ortholog PP_3205 shares 62.3% identity with Hsero_1011.

"Pairwise identity over aligned residue pairs: 62.3%"

PMID:23125118

Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1.

The fde operon is induced by naringenin and chrysin, and a mutation in fdeA, the first gene of the operon, abolishes naringenin degradation.

"We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids."