Bacterial naringenin A-ring degradation

The Fde-associated oxidative route in Pseudomonadota begins with naringenin hydroxylation and oxygenolytic A-ring cleavage. Herbaspirillum seropedicae SmR1 supplies FdeE/FdeC mutant and metabolite evidence, and purified FdeE establishes NADPH-dependent hydroxylation. Related loci and whole-cell phenotypes extend the comparison across alpha-, beta- and gammaproteobacteria. Six chemical steps retain the proposed KEGG R13074-R13079 sequence, with unverified late enzyme assignments explicitly separated from demonstrated entry chemistry. FdeD and FdeH are associated proteins whose reaction position and physiological necessity remain unresolved. Pseudomonas putida KT2440 and Bradyrhizobium diazoefficiens USDA110 provide sequence-grounded comparisons, not demonstrated complete pathway reconstructions.

MODULE:bacterial_flavonoid_degradationCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_flavonoid_degradation.yaml
flavonoid catabolic processGO:0046275
PMID:27059806
Genetic and functional characterization of a novel meta-pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1
Mutant and LC-MS/MS evidence establishes FdeE-dependent naringenin monooxygenation and FdeC-dependent A-ring dioxygenation in H. seropedicae.
PMID:39107441
Novel enzymatic route to the synthesis of C-8 hydroxyflavonoids including flavonols and isoflavones
Purified Hsero_1007 (HERSS) is an NADPH-dependent FAD monooxygenase that hydroxylates naringenin and other flavonoids at C-8.
PMID:23125118
Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1
The fde operon is induced by naringenin and chrysin, and fdeA and fdeR mutants cannot degrade naringenin.
KEGG:map00946
Degradation of flavonoids
KEGG supplies the R13074-R13079 reaction chain and K26179-K26185 Fde role assignments; the individual reaction records mark the chemistry as unclear.
file:HERSS/Hsero_1007/Hsero_1007-ai-review.yaml
Herbaspirillum seropedicae Hsero_1007 FdeE gene review
The review grounds the FdeE leaf to D8J0W9, GO:0016709 and flavonoid catabolic process, from mutant and purified-enzyme evidence.
file:HERSS/Hsero_1005/Hsero_1005-ai-review.yaml
Herbaspirillum seropedicae Hsero_1005 FdeC gene review
The review grounds the FdeC leaf to D8J0W7 and GO:0016702 from the fdeC mutant phenotype and removes the submitter glyoxalase II activity.
file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md
KEGG orthology and reaction assignments for the H. seropedicae fde locus
Live KEGG queries map Hsero_1004-Hsero_1012 to the Fde orthology groups K26179-K26185, list the R13074-R13079 reactions, and count the genomes carrying each Fde ortholog.
file:PSEPK/PP_3197/PP_3197-ai-review.yaml
Pseudomonas putida PP_3197 FdeC-like gene review
The review grounds the FdeC leaf to Q88I05, GO:0016702, and orthology to the experimentally tested Hsero_1005 protein.
file:PSEPK/PP_3199/PP_3199-ai-review.yaml
Pseudomonas putida PP_3199 FdeE-like gene review
The review grounds the FdeE leaf to Q88I03 and a conservative monooxygenase molecular-function term.
file:PSEPK/PP_3195/PP_3195-ai-review.yaml
Pseudomonas putida PP_3195 FdeB-like gene review
The review identifies Q88I07 as a candidate FdeB hydrolase while leaving ester specificity and native pathway participation unresolved.
file:PSEPK/PP_3206/PP_3206-ai-review.yaml
Pseudomonas putida PP_3206 FdeJ-like gene review
The review identifies Q88HZ6 as an FdeJ-like candidate, but its molecular function and native process participation remain unresolved; the inherited process proposal is retired.
file:PSEPK/PP_3204/PP_3204-ai-review.yaml
Pseudomonas putida PP_3204 FdeH-like gene review
The review identifies a FdeH-like cupin candidate without an established native step; its inherited process proposal is retired.
file:PSEPK/PP_3205/PP_3205-ai-review.yaml
Pseudomonas putida PP_3205 FdeI-like gene review
The review accepts only broad catalytic activity and leaves R13078/R13079 and native process participation unresolved; its inherited process proposal is retired.
PMID:31265361
The Modification of the Flavonoid Naringenin by Bradyrhizobium sp. Strain ORS285 Changes the nod Genes Inducer Function to a Growth Stimulator.
The cached abstract reports that naringenin-dependent growth persists after fde-operon deletion; the separately accessed full-text degradation phenotype is traced in the companion module-notes evidence.
file:analysis/module_audits/bacterial_flavonoid_degradation/taxonomy-snapshot.json
Dated KO census: 50 genomes coassign all seven groups, spanning 29 beta-, 16 gamma- and five alphaproteobacteria; coassignment is not biochemical validation.
PMID:17014487
Perception and modification of plant flavonoid signals by rhizosphere microorganisms.
The review proposes that flavonoids shape rhizosphere communities through carbon availability and toxicity; this is ecological context for catabolism.
PMID:26963713
Bacterial species involved in the conversion of dietary flavonoids in the human gut.
The review organizes intestinal flavonoid conversion by species, strains and enzymes; it is comparative background rather than an assay of Fde proteins.
PMID:37718389
Microbial degradation of plant toxins.
The review surveys genes and enzymes of plant-toxin breakdown; its broad ecological coverage does not establish a particular Fde reaction.
file:modules/bacterial_flavonoid_degradation-notes.md
Flavonoid module full-text access and comparative boundaries
The notes document separately accessed publisher Results/Figure 8 for PMID:31265361: ORS285 whole-fde deletion abolished the reported degradation phenotype while naringenin-dependent growth persisted. This is locus-level evidence, not an individual late-enzyme assay.

Scope is Pseudomonadota (NCBITaxon:1224), based on the experimentally studied Herbaspirillum route, independent ORS285 locus evidence, and a dated census spanning alpha-, beta- and gammaproteobacteria. All seven KO groups co-occur in 50 sampled genomes of this phylum; two Actinomycetota carry individual FdeE assignments. This bounds the present model without asserting universal absence elsewhere. KEGG coassignment and broad PANTHER hits alone do not establish pathway capacity. The 21 reviewed representative proteins span three classes; only HERSS has the step-specific assays used here. H. rubrisubalbicans M1 provides an additional phenotype but lacks a resolved UniProt mapping for its FdeE, so no other strain is substituted. PP_3199 retains sequence-based FdeE support although current KEGG gene and link queries no longer assign K26180; historical analysis is preserved. Family identifiers describe broader evolutionary groups, not substrate-specific Fde clades. The FdeC group has no common verified family identifier across its exemplars: BRADU Q89GB8 maps to PTHR21366:SF14, while HERSS lacks a PANTHER assignment. Keep that group as a sequence-grounded free-text family rather than applying the BRADU identifier to every member. FdeA insertion in the 2013 study was probably polar and did not establish autonomous FdeA chemistry. FdeG was mutated in the 2016 study, but its outcome is not accessible in the abstract; exclusion from assigned reaction steps is not evidence of dispensability. Optional FdeD/FdeH context parts encode unresolved dependence, not experimentally demonstrated deletion tolerance. The six-step chemical chain remains a hypothesis beyond the demonstrated entry; neither model satisfaction nor family membership establishes native flux. See the module notes and audit evidence for source access and assay boundaries. The complete inherited-process audit retires nine ungrounded B/D/H/I/J proposals while preserving their row payloads. FdeE/FdeC steps with experimental donor evidence and qualified ortholog inferences remain active. Optional-context and late chemical-role coverage do not reassert retired gene-level participation claims.

9Nodes
8Parts
0Variant Sets
0Variants
8Annotons
5Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_flavonoid_degradation deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • r13074_naringenin_hydroxylation → r13075_a_ring_cleavage [NOT_CHECKED]
    The R13074 product is the R13075 substrate in KEGG map00946. This verifies continuity within the proposed chemical scheme only; it does not verify native intermediates, enzyme assignment or pathway flux.
  • r13075_a_ring_cleavage → r13076_c_c_hydrolysis [NOT_CHECKED]
    The R13075 product C22569 is the R13076 substrate. This verifies continuity within the proposed chemical scheme only; it does not verify native intermediates, enzyme assignment or pathway flux.
  • r13076_c_c_hydrolysis → r13077_lactone_hydrolysis [NOT_CHECKED]
    R13076 produces the delta-lactone consumed by R13077. This verifies continuity within the proposed chemical scheme only; it does not verify native intermediates, enzyme assignment or pathway flux.
  • r13077_lactone_hydrolysis → r13078_decarboxylation [NOT_CHECKED]
    R13077 produces the beta-keto acid consumed by R13078. This verifies continuity within the proposed chemical scheme only; it does not verify native intermediates, enzyme assignment or pathway flux.
  • r13078_decarboxylation → r13079_dehydration [NOT_CHECKED]
    R13078 produces the hydroxyketone consumed by R13079. This verifies continuity within the proposed chemical scheme only; it does not verify native intermediates, enzyme assignment or pathway flux.

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 21 evidence or coverage gap(s) (32 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
fdee_monooxygenase Hsero_1007 (HERSS)
UniProtKB:D8J0W9
Family Representative 		flavonoid 8-monooxygenase activity
GO:0016709 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdee_monooxygenase PP_3199 (PSEPK)
UniProtKB:Q88I03
Family Representative 		flavonoid 8-monooxygenase activity
GO:0016709 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdee_monooxygenase bll6425 (BRADU)
UniProtKB:Q89GC0
Family Representative 		flavonoid 8-monooxygenase activity
GO:0016709 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdec_dioxygenase Hsero_1005 (HERSS)
UniProtKB:D8J0W7
Family Representative 		flavonoid A-ring extradiol dioxygenase activity
GO:0016702 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdec_dioxygenase PP_3197 (PSEPK)
UniProtKB:Q88I05
Family Representative 		flavonoid A-ring extradiol dioxygenase activity
GO:0016702 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdec_dioxygenase bll6427 (BRADU)
UniProtKB:Q89GB8
Family Representative 		flavonoid A-ring extradiol dioxygenase activity
GO:0016702 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdej_c_c_hydrolase Hsero_1012 (HERSS)
UniProtKB:D8J0X4
Family Representative 		predicted oxaloacetate-releasing cleavage of C22569 (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdej_c_c_hydrolase PP_3206 (PSEPK)
UniProtKB:Q88HZ6
Family Representative 		predicted oxaloacetate-releasing cleavage of C22569 (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdej_c_c_hydrolase bll6421 (BRADU)
UniProtKB:Q89GC4
Family Representative 		predicted oxaloacetate-releasing cleavage of C22569 (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdeb_ester_hydrolase Hsero_1004 (HERSS)
UniProtKB:D8J0W6
Family Representative 		flavonoid-derived delta-lactone hydrolase activity
GO:0052689 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
fdeb_ester_hydrolase PP_3195 (PSEPK)
UniProtKB:Q88I07
Family Representative 		flavonoid-derived delta-lactone hydrolase activity
GO:0052689 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
fdeb_ester_hydrolase bll6428 (BRADU)
UniProtKB:Q89GB7
Family Representative 		flavonoid-derived delta-lactone hydrolase activity
GO:0052689 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
fdei_decarboxylase Hsero_1011 (HERSS)
UniProtKB:D8J0X3
Family Representative 		predicted flavonoid-derived beta-keto acid decarboxylation (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdei_decarboxylase PP_3205 (PSEPK)
UniProtKB:Q88HZ7
Family Representative 		predicted flavonoid-derived beta-keto acid decarboxylation (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdei_decarboxylase bll6422 (BRADU)
UniProtKB:Q89GC3
Family Representative 		predicted flavonoid-derived beta-keto acid decarboxylation (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdei_dehydration_role Hsero_1011 (HERSS)
UniProtKB:D8J0X3
Family Representative 		predicted hydroxyketone dehydration (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdei_dehydration_role PP_3205 (PSEPK)
UniProtKB:Q88HZ7
Family Representative 		predicted hydroxyketone dehydration (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdei_dehydration_role bll6422 (BRADU)
UniProtKB:Q89GC3
Family Representative 		predicted hydroxyketone dehydration (no GO molecular function term asserted)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fded_rieske_partner Hsero_1006 (HERSS)
UniProtKB:D8J0W8
Family Representative 		2 iron, 2 sulfur cluster binding
GO:0051537 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fded_rieske_partner PP_3198 (PSEPK)
UniProtKB:Q88I04
Family Representative 		2 iron, 2 sulfur cluster binding
GO:0051537 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fded_rieske_partner bll6426 (BRADU)
UniProtKB:Q89GB9
Family Representative 		2 iron, 2 sulfur cluster binding
GO:0051537 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fdeh_cupin_component Hsero_1010 (HERSS)
UniProtKB:D8J0X2
Family Representative 		unresolved FdeH biochemical contribution (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdeh_cupin_component PP_3204 (PSEPK)
UniProtKB:Q88HZ8
Family Representative 		unresolved FdeH biochemical contribution (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdeh_cupin_component bll6423 (BRADU)
UniProtKB:Q89GC2
Family Representative 		unresolved FdeH biochemical contribution (no GO molecular function term)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fdee_monooxygenase FdeE naringenin monooxygenase family
PANTHER:PTHR13789:SF309
Family 		flavonoid 8-monooxygenase activity
GO:0016709 		Family Supported
Family review supports GO:0016709 for PANTHER:PTHR13789:SF309. FdeE (Hsero_1007, SF309) requires NADPH, and NicC (the KT2440 protein Q88FY2 in SF309 and the biochemically characterized Bordetella bronchiseptica RB50 protein A0A0H3LKL4 in SF318) uses NADH. Both use the reduced pyridine nucleotide and O2 to insert one oxygen atom, so the reaction class holds in SF309 and SF318 regardless of substrate. The SF318 PANTHER name ("geranylgeranyl diphosphate reductase") does not describe these members. The class is probably shared by the other subfamilies of this group A flavoprotein monooxygenase family, but they were not adjudicated in this review.
fdec_dioxygenase FdeC flavonoid A-ring dioxygenase family
Family 		flavonoid A-ring extradiol dioxygenase activity
GO:0016702 		Family Id Missing
The family has no identifier linking it to a curated family review.
fdej_c_c_hydrolase FdeJ flavonoid-cleavage-product hydrolase family
PANTHER:PTHR43103
Family 		predicted oxaloacetate-releasing cleavage of C22569 (no GO molecular function term)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
fdeb_ester_hydrolase FdeB flavonoid-derived lactone hydrolase family
PANTHER:PTHR22946
Family 		flavonoid-derived delta-lactone hydrolase activity
GO:0052689 		Family Function Unreviewed
Family review leaves GO:0052689 UNRESOLVED. Ester hydrolysis is characterized for FrsA-type and cutinase members and predicted for FdeB, but AYG1 and 2,6-dihydropseudooxynicotine hydrolase cleave carbon-carbon bonds, so the term is not family-wide and no subfamily boundary for it can be drawn from the local data.
fdei_decarboxylase FdeI late flavonoid-degradation enzyme family
PANTHER:PTHR43211
Family 		predicted flavonoid-derived beta-keto acid decarboxylation (no GO molecular function term asserted)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
fdei_dehydration_role FdeI late flavonoid-degradation enzyme family
PANTHER:PTHR43211
Family 		predicted hydroxyketone dehydration (no GO molecular function term asserted)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
fded_rieske_partner FdeD Rieske [2Fe-2S] protein family
PANTHER:PTHR40261
Family 		2 iron, 2 sulfur cluster binding
GO:0051537 		Family Supported
Family review supports GO:0051537 FAMILY_WIDE. The Rieske domain spans almost the entire length of the members examined, and the cluster-ligand residues are present in Hsero_1006.
fdeh_cupin_component FdeH cupin-family pathway component
PANTHER:PTHR36156
Family 		unresolved FdeH biochemical contribution (no GO molecular function term)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.

Gene-review completeness (21/21 grounded genes reviewed)

15 complete review(s) · 6 with deep research · 0 missing review · 15 reviewed but lacking deep research

Gene Review Complete Deep research
bll6421 Q89GC4 ✓ 0/0 ✗
bll6422 Q89GC3 ✓ ✓ ✗
bll6423 Q89GC2 ✓ 0/0 ✗
bll6425 Q89GC0 ✓ ✓ ✗
bll6426 Q89GB9 ✓ ✓ ✗
bll6427 Q89GB8 ✓ 2/3 ✗
bll6428 Q89GB7 ✓ 3/4 ✗
Hsero_1004 D8J0W6 ✓ 3/4 ✗
Hsero_1005 D8J0W7 ✓ ✓ ✗
Hsero_1006 D8J0W8 ✓ ✓ ✗
Hsero_1007 D8J0W9 ✓ ✓ ✗
Hsero_1010 D8J0X2 ✓ ✓ ✗
Hsero_1011 D8J0X3 ✓ ✓ ✗
Hsero_1012 D8J0X4 ✓ ✓ ✗
PP_3195 Q88I07 ✓ 3/4 ✓
PP_3197 Q88I05 ✓ ✓ ✓
PP_3198 Q88I04 ✓ ✓ ✗
PP_3199 Q88I03 ✓ ✓ ✓
PP_3204 Q88HZ8 ✓ ✓ ✓
PP_3205 Q88HZ7 ✓ ✓ ✓
PP_3206 Q88HZ6 ✓ ✓ ✓

Details

Context
PseudomonadotaNCBITaxon:1224
bacterial naringenin A-ring degradationMetabolic Pathwaybacterial_flavonoid_degradation
flavonoid catabolic processGO:0046275
Context
PseudomonadotaNCBITaxon:1224

Connections

KEGG:map00946
Reaction records supply the proposed chemical continuity; experimental confidence differs between entry and late steps.
KEGG:map00946
Reaction records supply the proposed chemical continuity; experimental confidence differs between entry and late steps.
KEGG:map00946
Reaction records supply the proposed chemical continuity; experimental confidence differs between entry and late steps.
KEGG:map00946
Reaction records supply the proposed chemical continuity; experimental confidence differs between entry and late steps.
KEGG:map00946
Reaction records supply the proposed chemical continuity; experimental confidence differs between entry and late steps.
Part 1: naringenin hydroxylation
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. HERSS entry chemistry has experimental support; comparative species specificity remains inferred.

naringenin to 5,7,8-trihydroxyflavanoneReactionr13074_naringenin_hydroxylation

Annotons

FdeE flavonoid monooxygenase
fdee_monooxygenase
Participant: Family: FdeE naringenin monooxygenase family
Family:
FdeE naringenin monooxygenase familyPANTHER:PTHR13789:SF309 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1007 (HERSS)UniProtKB:D8J0W9 PP_3199 (PSEPK)UniProtKB:Q88I03 bll6425 (BRADU)UniProtKB:Q89GC0

Function

flavonoid 8-monooxygenase activityGO:0016709
Substrates: naringenin dioxygen NADPH (demonstrated for HERSS FdeE; donor preference untested in comparative targets)
Products: 5,7,8-trihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one

FdeE catalyzes the experimentally supported entry monooxygenation in HERSS. Comparative targets support the NAD(P)H-dependent reaction class, but naringenin specificity, C8 regioselectivity and native flux remain inferred. Purified-enzyme substrate breadth does not establish complete catabolism of each accepted flavonoid.

file:BRADU/bll6425/bll6425-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part 2: oxygenolytic A-ring cleavage
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. HERSS entry chemistry has experimental support; comparative species specificity remains inferred.

trihydroxyflavanone dioxygenation and A-ring cleavageReactionr13075_a_ring_cleavage

Annotons

FdeC A-ring-cleaving dioxygenase
fdec_dioxygenase
Participant: Family: FdeC flavonoid A-ring dioxygenase family
Family:
FdeC flavonoid A-ring dioxygenase family Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1005 (HERSS)UniProtKB:D8J0W7 PP_3197 (PSEPK)UniProtKB:Q88I05 bll6427 (BRADU)UniProtKB:Q89GB8

Function

flavonoid A-ring extradiol dioxygenase activityGO:0016702
Substrates: 5,7,8-trihydroxyflavanone dioxygen
Products: A-ring meta-cleavage product C22569

FdeC is the experimentally supported ring-cleavage catalyst; substrate- specific chemistry in species other than H. seropedicae remains inferred.

file:BRADU/bll6427/bll6427-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part 3: cleavage-product hydrolysis
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. The named Fde carrier and exact substrate remain hypotheses; this required chemical role is not proof that the named gene is necessary in vivo.

proposed C22569 to flavonoid-derived delta-lactone and oxaloacetateReactionr13076_c_c_hydrolysis

Annotons

FdeJ pathway component
fdej_c_c_hydrolase
Participant: Family: FdeJ flavonoid-cleavage-product hydrolase family
Family:
FdeJ flavonoid-cleavage-product hydrolase familyPANTHER:PTHR43103 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1012 (HERSS)UniProtKB:D8J0X4 PP_3206 (PSEPK)UniProtKB:Q88HZ6 bll6421 (BRADU)UniProtKB:Q89GC4

Function

predicted oxaloacetate-releasing cleavage of C22569 (no GO molecular function term) KEGG R13076 converts the A-ring cleavage product to a delta-lactone and oxaloacetate; KEGG marks the reaction as unclear and FdeJ has an NAD(P)-dependent epimerase/dehydratase fold, so no GO identifier is asserted.
Substrates: A-ring meta-cleavage product C22569 water
Products: 5-(4-hydroxyphenyl)-3-oxovalero-delta-lactone oxaloacetate

KEGG assigns FdeJ to the oxaloacetate-releasing R13076 step, but no FdeJ-family protein has been characterized for this reaction and the epimerase/dehydratase fold does not establish carbon-carbon hydrolase chemistry. No molecular-function term is asserted.

file:BRADU/bll6421/bll6421-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part 4: delta-lactone ring opening
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. The named Fde carrier and exact substrate remain hypotheses; this required chemical role is not proof that the named gene is necessary in vivo.

proposed flavonoid-derived delta-lactone hydrolysisReactionr13077_lactone_hydrolysis

Annotons

FdeB predicted lactone hydrolysis
fdeb_ester_hydrolase
Participant: Family: FdeB flavonoid-derived lactone hydrolase family
Family:
FdeB flavonoid-derived lactone hydrolase familyPANTHER:PTHR22946 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1004 (HERSS)UniProtKB:D8J0W6 PP_3195 (PSEPK)UniProtKB:Q88I07 bll6428 (BRADU)UniProtKB:Q89GB7

Function

flavonoid-derived delta-lactone hydrolase activityGO:0052689
Substrates: 5-(4-hydroxyphenyl)-3-oxovalero-delta-lactone water
Products: 5-hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate

KEGG proposes FdeB for R13077, but all three representative reviews leave ester-versus-C-C hydrolysis and native pathway participation unresolved. GO:0052689 describes the hypothetical ester-hydrolysis reaction role, not a validated function of the representative proteins. Model coverage identifies candidate carriers and must not be exported as evidence of their activity.

file:BRADU/bll6428/bll6428-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part 5: beta-keto acid decarboxylation
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. The named Fde carrier and exact substrate remain hypotheses; this required chemical role is not proof that the named gene is necessary in vivo.

proposed flavonoid-derived beta-keto acid decarboxylationReactionr13078_decarboxylation

Annotons

FdeI predicted decarboxylation
fdei_decarboxylase
Participant: Family: FdeI late flavonoid-degradation enzyme family
Family:
FdeI late flavonoid-degradation enzyme familyPANTHER:PTHR43211 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1011 (HERSS)UniProtKB:D8J0X3 PP_3205 (PSEPK)UniProtKB:Q88HZ7 bll6422 (BRADU)UniProtKB:Q89GC3

Function

predicted flavonoid-derived beta-keto acid decarboxylation (no GO molecular function term asserted) KEGG R13078 removes CO2 from the flavonoid-derived beta-keto acid and assigns the step to FdeI, but KEGG marks the reaction as unclear and no FdeI-family protein has been assayed. The FAH fold supports hydrolases, decarboxylases, isomerases and hydratases, so no carboxy-lyase GO term is asserted, matching FdeH and FdeJ.
Substrates: 5-hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate
Products: 4-hydroxy-4-(4-hydroxyphenyl)-butan-2-one carbon dioxide

FdeI is the predicted decarboxylase for R13078 (KEGG K26185), but no direct FdeI-family assay has established the reaction or any reaction class.

file:BRADU/bll6422/bll6422-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part 6: water elimination
PMID:27059806
Entry mutant/metabolite evidence and oxaloacetate production frame the route; the accessible abstract does not establish every downstream enzyme assignment.

Chemical step in the proposed R13074-R13079 route. The named Fde carrier and exact substrate remain hypotheses; this required chemical role is not proof that the named gene is necessary in vivo.

proposed hydroxyketone to 4-hydroxycinnamoylmethaneReactionr13079_dehydration

Annotons

unresolved FdeI-associated dehydration
fdei_dehydration_role
Participant: Family: FdeI late flavonoid-degradation enzyme family
Family:
FdeI late flavonoid-degradation enzyme familyPANTHER:PTHR43211 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1011 (HERSS)UniProtKB:D8J0X3 PP_3205 (PSEPK)UniProtKB:Q88HZ7 bll6422 (BRADU)UniProtKB:Q89GC3

Function

predicted hydroxyketone dehydration (no GO molecular function term asserted) KEGG R13079 eliminates water from 4-hydroxy-4-(4-hydroxyphenyl)-butan-2-one; whether FdeI, another protein, or no enzyme performs it is unknown, so no hydro-lyase term is asserted.
Substrates: 4-hydroxy-4-(4-hydroxyphenyl)-butan-2-one
Products: 4-hydroxycinnamoylmethane water

KEGG assigns R13079 to FdeI, but available evidence does not establish whether PP_3205 catalyzes water elimination or whether this conversion is spontaneous or performed by another factor. No MF term is asserted.

file:BRADU/bll6422/bll6422-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part: unresolved locus-associated contribution (optional)
FdeD Rieske electron-transfer componentMolecular Functionfded_unresolved_locus_role

Its locus association is retained, but exact position and physiological requirement are unknown. Optionality avoids asserting an unsupported obligatory partner; it is not a deletion phenotype.

Annotons

FdeD Rieske locus-associated protein
fded_rieske_partner
Participant: Family: FdeD Rieske [2Fe-2S] protein family
Family:
FdeD Rieske [2Fe-2S] protein familyPANTHER:PTHR40261 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1006 (HERSS)UniProtKB:D8J0W8 PP_3198 (PSEPK)UniProtKB:Q88I04 bll6426 (BRADU)UniProtKB:Q89GB9

Function

2 iron, 2 sulfur cluster bindingGO:0051537

Rieske cofactor binding is supported. The donor, acceptor and pathway position are unknown. Purified HERSS FdeE acts with NADPH without added FdeD, so entry hydroxylation does not require an asserted FdeD-to-FdeE relay. Another physiological role remains possible.

file:BRADU/bll6426/bll6426-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.
Part: unresolved locus-associated contribution (optional)
FdeH cupin componentMolecular Functionfdeh_unresolved_locus_role

Its locus association is retained, but exact position and physiological requirement are unknown. Optionality avoids asserting an unsupported obligatory partner; it is not a deletion phenotype.

Annotons

FdeH cupin component
fdeh_cupin_component
Participant: Family: FdeH cupin-family pathway component
Family:
FdeH cupin-family pathway componentPANTHER:PTHR36156 Sequence-related Fde-locus proteins; the database family, where present, is broader than this role and does not establish the specific substrate or complete pathway.
Representative Members: Hsero_1010 (HERSS)UniProtKB:D8J0X2 PP_3204 (PSEPK)UniProtKB:Q88HZ8 bll6423 (BRADU)UniProtKB:Q89GC2

Function

unresolved FdeH biochemical contribution (no GO molecular function term) Cupin type-2 protein KEGG-co-assigned with FdeC to R13075. No catalytic, metal-binding or structural activity has been shown, so no GO identifier is asserted.

KEGG coassignment to R13075 is a hypothesis. Variovorax IfcD1/D2 cupins act farther downstream in a related isoflavone route, motivating investigation of FdeH position. Direct equivalence and native FdeH substrate are unestablished; do not require FdeH as a FdeC ring-cleavage partner.

file:BRADU/bll6423/bll6423-ai-review.yaml
Alphaproteobacterial comparison; supports family membership and explicitly bounded functional inference, not a measured USDA110 realization of this exact step.