Gene Ontology annotation based on Enzyme Commission mapping

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

The steps after A-ring cleavage release 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_1012/Hsero_1012-uniprot.txt

UniProtKB entry D8J0X4 for Herbaspirillum seropedicae SmR1 Hsero_1012

The protein has the NAD-dependent epimerase/dehydratase domain on a Rossmann fold.

"InterPro; IPR001509; Epimerase_deHydtase."

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

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

KEGG assigns Hsero_1012 to FdeJ (K26183) and UDP-glucose 4-epimerase in SmR1 to other genes.

"KEGG mapping: `hse:Hsero_1012 -> ko:K26183` (fdeJ; naringenin degradation protein FdeJ)"

file:PSEPK/PP_3206/PP_3206-bioinformatics/RESULTS.md

Reproducible PP_3206 and Hsero_1012 FdeJ sequence comparison

The P. putida ortholog PP_3206 shares 51.1% identity with Hsero_1012.

"Pairwise identity over aligned residue pairs: 51.1%"

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."