Bacterial fatty acid beta-oxidation spiral

A four-reaction bacterial mechanism that converts an accepted fatty acyl-CoA into acetyl-CoA and a two-carbon-shorter acyl-CoA. Dehydrogenation, hydration, NAD-dependent oxidation and thiolysis are implemented by distinct enzyme families and compatible multifunctional complexes. The sampled enterobacterial, pseudomonad, mycobacterial and Bacillus systems differ in assembly, substrate range, electron-transfer evidence and native endpoint. Fatty-acid transport/activation, cofactor recycling, unsaturated-substrate auxiliary reactions and odd-chain product disposal are external requirements rather than hidden steps of this core.

MODULE:bacterial_fatty_acid_beta_oxidationCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_fatty_acid_beta_oxidation.yaml
fatty acid beta-oxidationGO:0006635

Comparative scientific review complete; publication and merge gates are tracked separately. Nineteen reviewed member proteins ground the four required reactions through eight families. The enterobacterial/putida and PAO1 first-step implementations use acceptor-unspecified activities because their physiological electron relays remain unresolved. Bacillus separately uses an inferred ETF-linked GO:0003995 activity. Acceptor uncertainty does not erase supported chain-length specificity. Compiler satisfiability represents the four chemical roles; compatible partner, substrate, cofactor and evidence-level conditions are separately checked by curated endpoint witnesses. Gene review rows are preserved, including inherited proposals; no phenotype is silently promoted to isolated kinetics. Hydratase core-term convention: use the most specific term that covers the supported reaction repertoire. BACSU FadB is represented by GO:0018812 for assayed 2-enoyl-CoA hydration; ECOLI FadB retains GO:0004300 because its supported repertoire also includes the distinct (3E)-enoyl-CoA hydration represented by RHEA:20724. GO:0018812 alone would omit that latter reaction. Neither choice asserts an unmeasured chain-length range. BACSU FadE is an explicitly inferred ETF-linked realization supported by native yusJ/etfAB genetics and protein-family evidence. This differs from the unresolved enterobacterial/PAO1 relays; absence of direct reconstitution alone is not a universal veto. Acceptor-unspecified proposals retain long/medium or C4/medium specificity in the respective gene reviews.

15Nodes
4Parts
4Variant Sets
10Variants
10Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_fatty_acid_beta_oxidation 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.

Function consistency and core coverage

16 gene-function check(s) reflected in core functions · 0 conflict(s) · 14 evidence or coverage gap(s) (34 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
fade_acyl_coa_dehydrogenase_activity fadE (PSEPK)
UniProtKB:Q88LN6
Family Representative 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fade_acyl_coa_dehydrogenase_activity fadE (ECOLI)
UniProtKB:Q47146
Family Representative 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
fade_acyl_coa_dehydrogenase_activity fadE (SALTY)
UniProtKB:Q8ZRJ7
Family Representative 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
pao1_fade1_fade2 PA0506 (PSEAE)
UniProtKB:Q9I612
Family Representative 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
pao1_fade1_fade2 PA0508 (PSEAE)
UniProtKB:Q9I610
Family Representative 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
bacillus_fade fadE (BACSU)
UniProtKB:O32176
Family Representative 		acyl-CoA dehydrogenase activity
GO:0003995 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_enoyl_coa_hydratase_activity fadB (PSEPK)
UniProtKB:Q88L02
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
fadb_enoyl_coa_hydratase_activity fadB (ECOLI)
UniProtKB:P21177
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
fadb_enoyl_coa_hydratase_activity fadB (SALTY)
UniProtKB:Q9L6L5
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
fadb_enoyl_coa_hydratase_activity fadB (PSEFR)
UniProtKB:P28793
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_enoyl_coa_hydratase_activity fadB (MYCTU)
UniProtKB:O53872
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacillus_fadb_hydratase fadB (BACSU)
UniProtKB:P94549
Family Representative 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_hydroxyacyl_coa_dehydrogenase_activity fadB (PSEPK)
UniProtKB:Q88L02
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_hydroxyacyl_coa_dehydrogenase_activity fadB (ECOLI)
UniProtKB:P21177
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_hydroxyacyl_coa_dehydrogenase_activity fadB (SALTY)
UniProtKB:Q9L6L5
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_hydroxyacyl_coa_dehydrogenase_activity fadB (PSEFR)
UniProtKB:P28793
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fadb_hydroxyacyl_coa_dehydrogenase_activity fadB (MYCTU)
UniProtKB:O53872
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacillus_fadn_dehydrogenase fadN (BACSU)
UniProtKB:O32178
Family Representative 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fada_ketoacyl_coa_thiolase_activity fadA__Q88L01 (PSEPK)
UniProtKB:Q88L01
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fada_ketoacyl_coa_thiolase_activity fadA (ECOLI)
UniProtKB:P21151
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fada_ketoacyl_coa_thiolase_activity fadA (SALTY)
UniProtKB:P0A2H7
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fada_ketoacyl_coa_thiolase_activity fadA (PSEFR)
UniProtKB:P28790
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mycobacterial_fada_thiolase fadA (MYCTU)
UniProtKB:O53871
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacillus_fada_thiolase fadA (BACSU)
UniProtKB:O32177
Family Representative 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fade_acyl_coa_dehydrogenase_activity Extended bacterial FadE
PANTHER:PTHR48083:SF18
Family 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
pao1_fade1_fade2 PAO1 FadE1/FadE2
PANTHER:PTHR42803:SF1
Family 		acyl-CoA dehydrogenase activity (acceptor unspecified)
No function ID 		No Function Id
The family function has no GO identifier for comparison; prose is not matched.
bacillus_fade Bacillus FadE
PANTHER:PTHR43884:SF12
Family 		acyl-CoA dehydrogenase activity
GO:0003995 		Family Function Unreviewed
Family review leaves GO:0003995 UNRESOLVED. The inventory extends beyond acyl-CoA dehydrogenases to nitroalkane oxidases, monooxygenases and desulfinases; even SF12 mixes different reactions. Within the ACAD9 branch, direct protein-interaction studies show ECSIT-induced deflavination and loss of dehydrogenase activity during complex-I assembly (PMID:34646991). Catalytic potential and assembly function are alternative biochemical states, not evidence of constitutive pseudoenzyme inactivity. Neither substrate specificity nor complex-I assembly transfers to the entire family. A complete set of function-bearing branches is not delimited, so no exhaustive family or subfamily grant is asserted. For BACSU FadE O32176 in SF12, convergent yusJ and etfAB regulatory/growth phenotypes plus enzyme/ETF identities support a target-specific inferred ETF-linked activity, now accepted in the gene review. Direct transfer between isolated proteins remains unmeasured. That target inference does not delimit every function-bearing branch of this mixed family.
fadb_enoyl_coa_hydratase_activity Multifunctional FadB alpha-chain hydration
PANTHER:PTHR43612:SF3
Family 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Family Supported
Family review supports GO:0018812 for PANTHER:PTHR43612:SF3. SF3 multifunctional alpha chains support the reversible 2E-enoyl-CoA/3S-hydroxyacyl-CoA reaction. The pathway direction is hydration. This grant does not cover every auxiliary isomerization/epimerization, uniform chain-length preference or partner interchangeability. Direct bacterial studies and the conserved catalytic architecture support the specific reaction.
bacillus_fadb_hydratase Bacillus FadB hydration
PANTHER:PTHR11941:SF175
Family 		3-hydroxyacyl-CoA dehydratase activity
GO:0018812 		Family Scope Restricted
GO:0004300 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. Established for ECHS1 and PaaF (SF54) and, weakly, for AUH (SF12). SF54 also contains ScpB, a methylmalonyl-CoA decarboxylase, which is excepted; CaiD (crotonobetainyl-CoA hydratase, which also hydrates crotonyl-CoA slowly) is a hydratase and is not excepted. Because SF54 is broader than the PaaF role, the phenylacetate_catabolism module selects the PaaF step with the paa-specific NCBIfam model NCBIfam:NF007239 rather than with SF54. Merge reconciliation: SF175 is added because Bacillus subtilis FadB (P94549, SF175) hydrates crotonyl-CoA in a direct assay. This is the positive member behind the fatty-acid review's GO:0018812 entry; that entry stays UNRESOLVED for SF175 as a whole, so SF175 is listed here for the parent activity only.
fadb_hydroxyacyl_coa_dehydrogenase_activity Multifunctional FadB alpha-chain oxidation
PANTHER:PTHR43612:SF3
Family 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Family Supported
Family review supports GO:0003857 FAMILY_WIDE. The C-terminal dehydrogenase domain and its catalytic histidine are conserved throughout; the long-chain child GO:0016509 is root-placed by PAINT.
bacillus_fadn_dehydrogenase Bacillus FadN oxidation
PANTHER:PTHR48075:SF7
Family 		(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
GO:0003857 		Family Function Unreviewed
Family review leaves GO:0003857 UNRESOLVED. UNRESOLVED. The activity is established for named members (PaaH in SF5, FadB2 in SF9, FadN in SF7), but SF5 also holds the L-carnitine dehydrogenases, so no subfamily grant is safe. Positive named-member evidence supports Bacillus FadN O32178: curated reaction, NAD/dehydrogenase domains and native yusL palmitate genetics. The additional hydratase domain is not itself a target hydration assay. Neither this member nor the SF7 label establishes the substrate and reaction for every SF7 member, much less the mixed carnitine/gulonate/acyl-CoA family. No new exact-reaction PAINT node is inferred from the broad PTN002455225 oxidoreductase assertion. Established for PaaH (SF5; NAD+, (S)-3-hydroxyadipyl-CoA) and consistent with FadB2 (SF9). Not applicable to the L-gulonate 3-dehydrogenases (SF1). SF5 also contains bacterial L-carnitine dehydrogenases, so within SF5 the term should be confirmed per member rather than inherited. Merge reconciliation: UNRESOLVED from the fatty-acid review is kept. SF5 also holds the L-carnitine dehydrogenases, so the branch's SF5/SF9 SUBFAMILY_ONLY grant would over-reach. The phenylacetate module no longer selects this family for PaaH; it uses NCBIfam TIGR02279.
fada_ketoacyl_coa_thiolase_activity Classical FadA beta-chain thiolysis
PANTHER:PTHR43853:SF11
Family 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Family Supported
Family review supports GO:0003988 FAMILY_WIDE. Asserted by peroxisomal_beta_oxidation, phenylacetate_catabolism and bacterial_fatty_acid_beta_oxidation; accepted by every reviewed member. 3-oxoacyl-CoA thiolysis is shared by all characterized members, including PaaJ (SF2).
mycobacterial_fada_thiolase H37Rv FadA thiolysis
PANTHER:PTHR43365:SF1
Family 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Family Function Unreviewed
Family review leaves GO:0003985 UNRESOLVED. O53871 does not have demonstrated acetoacetyl-CoA thiolysis under the reported assay, so this C4-specific function is not granted to that member. Family and SF1 classifications alone cannot specify substrates, partner requirements or pathways for all members. The reviewed-entry list includes FadA, FadA5 and FadA6 in the same SF1, and the current eight-leaf tree does not resolve the PAINT nodes or O53871. Preserve UNRESOLVED scope rather than an unsupported whole-subfamily grant or denial. No evolutionary-loss claim or unconditional negative member exception is made.
bacillus_fada_thiolase Bacillus FadA thiolysis
PANTHER:PTHR43853:SF21
Family 		acetyl-CoA C-acyltransferase activity
GO:0003988 		Family Supported
Family review supports GO:0003988 FAMILY_WIDE. Asserted by peroxisomal_beta_oxidation, phenylacetate_catabolism and bacterial_fatty_acid_beta_oxidation; accepted by every reviewed member. 3-oxoacyl-CoA thiolysis is shared by all characterized members, including PaaJ (SF2).

Gene-review completeness (19/19 grounded genes reviewed)

10 complete review(s) · 2 with deep research · 0 missing review · 17 reviewed but lacking deep research

Gene Review Complete Deep research
fadA O32177 ✓ 7/9 ✗
fadA O53871 ✓ 5/6 ✗
fadA P0A2H7 ✓ 9/10 ✗
fadA P21151 ✓ 20/21 ✗
fadA P28790 ✓ 10/11 ✗
fadA Q88L01 ✓ 8/9 ✗
fadB O53872 ✓ 10/11 ✗
fadB P21177 ✓ ✓ ✗
fadB P28793 ✓ ✓ ✗
fadB P94549 ✓ ✓ ✗
fadB Q88L02 ✓ 14/15 ✓
fadB Q9L6L5 ✓ ✓ ✗
fadE O32176 ✓ ✓ ✗
fadE Q47146 ✓ ✓ ✗
fadE Q88LN6 ✓ 5/8 ✓
fadE Q8ZRJ7 ✓ ✓ ✗
fadN O32178 ✓ ✓ ✗
PA0506 Q9I612 ✓ ✓ ✗
PA0508 Q9I610 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
activated fatty acyl-CoA supplied compatible enzymes and substrate chain length oxidized cofactors, CoA and electron-acceptor recycling available

Bacteria is the shared reaction-level scope supported by sampled Pseudomonadota, Actinomycetota and Bacillota implementations. It is not a distribution assertion for every bacterium or a claim that any family hit suffices. Strain, assay, partner and chain-length qualifications remain attached to the leaves and endpoint witnesses.

Bacterial fatty acid beta-oxidation spiralMetabolic Pathwaybacterial_fatty_acid_beta_oxidation
fatty acid beta-oxidationGO:0006635
Context
bacteriaNCBITaxon:2
activated fatty acyl-CoA supplied compatible enzymes and substrate chain length oxidized cofactors, CoA and electron-acceptor recycling available

Bacteria is the shared reaction-level scope supported by sampled Pseudomonadota, Actinomycetota and Bacillota implementations. It is not a distribution assertion for every bacterium or a claim that any family hit suffices. Strain, assay, partner and chain-length qualifications remain attached to the leaves and endpoint witnesses.

Connections

trans-(2E)-enoyl-CoA is the shared chemical intermediate when both selected enzymes accept the same chain.
PMID:35892328
The reviewed bacterial sequence connects acyl-CoA dehydrogenation to enoyl-CoA hydration; the physiological electron relay is unresolved.
(3S)-3-hydroxyacyl-CoA is the shared chemical intermediate when both selected enzymes accept the same chain.
PMID:368024
The E. coli multienzyme activities establish the sequential hydration, hydroxyacyl oxidation and thiolysis chemistry.
PMID:34371166
Substrate-resolved TFE assays bound continuity to accepted intermediates; they do not certify arbitrary cross-species enzyme combinations.
3-oxoacyl-CoA is the shared chemical intermediate when both selected enzymes accept the same chain.
PMID:368024
The E. coli multienzyme activities establish the sequential hydration, hydroxyacyl oxidation and thiolysis chemistry.
PMID:34371166
Substrate-resolved TFE assays bound continuity to accepted intermediates; they do not certify arbitrary cross-species enzyme combinations.
The shortened acyl-CoA can re-enter only while it remains an accepted substrate; acetyl-CoA is an exit product.
PMID:35892328
The spiral repeats only for a shortened chain accepted by the next cycle; acetyl-CoA exits.
file:MYCTU/fadB/fadB-source-analysis/primary-scope.md
The H37Rv substrate survey does not establish uninterrupted shortening through acetoacetyl-CoA.
Part 1: Fatty acyl-CoA dehydrogenation
Fatty acyl-CoA dehydrogenationReactionbacterial_acyl_coa_dehydrogenation

FAD-dependent desaturation to trans-2-enoyl-CoA. Enzyme-bound flavin and the downstream physiological electron-transfer partner are distinct; recycling must be supplied for sustained turnover.

Variant set: Supported protein implementations by verified family and representative protein [Realizer] (One Or More)
Extended bacterial FadEReactionfade_acyl_coa_dehydrogenase_activity_implementation

Annotons

Extended bacterial FadE
fade_acyl_coa_dehydrogenase_activity
Participant: Family: Extended bacterial FadE
Family:
Extended bacterial FadEPANTHER:PTHR48083:SF18 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadE (PSEPK)UniProtKB:Q88LN6 fadE (ECOLI)UniProtKB:Q47146 fadE (SALTY)UniProtKB:Q8ZRJ7

Function

acyl-CoA dehydrogenase activity (acceptor unspecified)
Substrates: 2,3-saturated fatty acyl-CoA oxidized electron acceptor (identity unresolved)
Products: trans-(2E)-enoyl-CoA reduced electron acceptor (identity unresolved)

Processes

fatty acid beta-oxidationGO:0006635

E. coli and LT2 genetics support participation; KT2440 PP1893 is a conserved-role inference. Bound FAD does not identify the physiological electron acceptor. The ETF-specific GO and Rhea reactions are deliberately not asserted.

PMID:12057976
FadE gene identification and complementation establish a pathway role.
PMID:16385050
LT2 FadE exchange changes whole-cell substrate processing.
file:PSEPK/fadB/fadB-source-analysis/primary-scope.md
PP1893 is not the strongest native KT2440 fatty-acid dehydrogenase candidate.
PMID:35892328
Physiological electron-transfer partner remains unresolved.
PAO1 FadE1/FadE2Reactionpao1_fade1_fade2_implementation

Annotons

PAO1 FadE1/FadE2
pao1_fade1_fade2
Participant: Family: PAO1 FadE1/FadE2
Family:
PAO1 FadE1/FadE2PANTHER:PTHR42803:SF1 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: PA0506 (PSEAE)UniProtKB:Q9I612 PA0508 (PSEAE)UniProtKB:Q9I610

Function

acyl-CoA dehydrogenase activity (acceptor unspecified)
Substrates: 2,3-saturated fatty acyl-CoA oxidized electron acceptor (identity unresolved)
Products: trans-(2E)-enoyl-CoA reduced electron acceptor (identity unresolved)

Processes

fatty acid beta-oxidationGO:0006635

Direct PAO1 recombinant enzyme assays use ferrocenium. FadE1 favors longer substrates; FadE2 is active on C4/C6/C8 and has no detected C16/C18 activity in the assay. FadE1 C4 was not determined. PA14 growth, Pa10348 proteomics and PAO1 virulence experiments are separate contexts; no uniform SF1 substrate window or ETF coupling follows.

PMID:40057486
PAO1-derived purified enzymes and engineered mutants separate catalytic competence, chain preference and physiological assay strain.
Bacillus FadEReactionbacillus_fade_implementation

Annotons

Bacillus FadE
bacillus_fade
Participant: Family: Bacillus FadE
Family:
Bacillus FadEPANTHER:PTHR43884:SF12 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadE (BACSU)UniProtKB:O32176

Function

acyl-CoA dehydrogenase activityGO:0003995
Substrates: 2,3-saturated fatty acyl-CoA oxidized electron-transfer flavoprotein (inferred native coupling)
Products: trans-(2E)-enoyl-CoA reduced electron-transfer flavoprotein (inferred native coupling)

Processes

fatty acid beta-oxidationGO:0006635

Strain168 yusJ and etfAB perturbations produce convergent regulatory and palmitate-use phenotypes. With enzyme/ETF family evidence, these support an inferred ETF-linked oxidation step; direct cognate protein electron transfer and complete substrate breadth remain unmeasured. The isovaleryl-related family label does not assign that substrate to FadE.

PMID:17189250
Palmitate utilization and ETF-associated perturbations support target pathway involvement with explicit genetic scope.
Part 2: trans-2-Enoyl-CoA hydration
trans-2-Enoyl-CoA hydrationReactionbacterial_enoyl_coa_hydration

Hydration yields the hydroxyacyl intermediate. The same multifunctional alpha chain also performs step3 in the classical complexes; family presence is not evidence that arbitrary chains or partners are compatible.

Variant set: Supported protein implementations by verified family and representative protein [Realizer] (One Or More)
Multifunctional FadB alpha-chain hydrationReactionfadb_enoyl_coa_hydratase_activity_implementation

Annotons

Multifunctional FadB alpha-chain hydration
fadb_enoyl_coa_hydratase_activity
Participant: Family: Multifunctional FadB alpha-chain hydration
Family:
Multifunctional FadB alpha-chain hydrationPANTHER:PTHR43612:SF3 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadB (PSEPK)UniProtKB:Q88L02 fadB (ECOLI)UniProtKB:P21177 fadB (SALTY)UniProtKB:Q9L6L5 fadB (PSEFR)UniProtKB:P28793 fadB (MYCTU)UniProtKB:O53872

Function

3-hydroxyacyl-CoA dehydratase activityGO:0018812
Substrates: trans-(2E)-enoyl-CoA water
Products: (3S)-3-hydroxyacyl-CoA

Processes

fatty acid beta-oxidationGO:0006635

The reversible GO reaction is used in its hydration direction. Direct E. coli/P. fragi/H37Rv evidence and curated LT2/KT2440 inference support the 2E reaction. Auxiliary epimerase/isomerase activities and chain-length preferences are not transferred wholesale.

PMID:368024
E. coli purified complex contains the hydration step.
PMID:9396725
P. fragi isolated alpha remains catalytically active.
PMID:34371166
H37Rv alpha carries ECH/HAD activities with substrate limits.
Bacillus FadB hydrationReactionbacillus_fadb_hydratase_implementation

Annotons

Bacillus FadB hydration
bacillus_fadb_hydratase
Participant: Family: Bacillus FadB hydration
Family:
Bacillus FadB hydrationPANTHER:PTHR11941:SF175 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadB (BACSU)UniProtKB:P94549

Function

3-hydroxyacyl-CoA dehydratase activityGO:0018812
Substrates: trans-(2E)-enoyl-CoA water
Products: (3S)-3-hydroxyacyl-CoA

Processes

fatty acid beta-oxidationGO:0006635

Direct recombinant168 FadB hydration is measured with crotonyl-CoA; the specific reversible reaction is consistent with curated mapping. The assay does not independently resolve product stereochemistry or establish a broad chain-length range. FadN contains an additional hydratase domain, but its hydration activity is not asserted here without resolved evidence.

file:BACSU/fadB/fadB-source-analysis/direct-assay.md
Purified His-tagged FadB hydrates crotonyl-CoA; native flux and substrate-window extrapolations remain separate.
Part 3: NAD-dependent hydroxyacyl-CoA oxidation
NAD-dependent hydroxyacyl-CoA oxidationReactionbacterial_hydroxyacyl_coa_oxidation

Forms the 3-oxoacyl-CoA consumed in thiolysis, requiring an available oxidized NAD pool.

Variant set: Supported protein implementations by verified family and representative protein [Realizer] (One Or More)
Multifunctional FadB alpha-chain oxidationReactionfadb_hydroxyacyl_coa_dehydrogenase_activity_implementation

Annotons

Multifunctional FadB alpha-chain oxidation
fadb_hydroxyacyl_coa_dehydrogenase_activity
Participant: Family: Multifunctional FadB alpha-chain oxidation
Family:
Multifunctional FadB alpha-chain oxidationPANTHER:PTHR43612:SF3 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadB (PSEPK)UniProtKB:Q88L02 fadB (ECOLI)UniProtKB:P21177 fadB (SALTY)UniProtKB:Q9L6L5 fadB (PSEFR)UniProtKB:P28793 fadB (MYCTU)UniProtKB:O53872

Function

(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activityGO:0003857
Substrates: (3S)-3-hydroxyacyl-CoA NAD+
Products: 3-oxoacyl-CoA NADH proton

Processes

fatty acid beta-oxidationGO:0006635

Uses the same compatible alpha chain as hydration. NAD+ reduction is supported; native cofactor regeneration and uniform long/short-chain throughput are not implied.

PMID:368024
E. coli purified complex combines hydroxyacyl oxidation with hydration and thiolysis.
PMID:34371166
H37Rv coupled ECH/HAD assays distinguish medium/long-chain activity from short-substrate limits.
Bacillus FadN oxidationReactionbacillus_fadn_dehydrogenase_implementation

Annotons

Bacillus FadN oxidation
bacillus_fadn_dehydrogenase
Participant: Family: Bacillus FadN oxidation
Family:
Bacillus FadN oxidationPANTHER:PTHR48075:SF7 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadN (BACSU)UniProtKB:O32178

Function

(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activityGO:0003857
Substrates: (3S)-3-hydroxyacyl-CoA NAD+
Products: 3-oxoacyl-CoA NADH proton

Processes

fatty acid beta-oxidationGO:0006635

Curated catalytic/domain assignment is corroborated by native palmitate genetics. A purified FadN specificity survey was not recovered. Its additional hydratase domain is acknowledged without treating the target as monofunctional or inventing measured hydratase turnover.

PMID:17189250
The yusL/fadN perturbation affects palmitate utilization; this is native pathway evidence rather than isolated kinetics.
Part 4: Thiolytic two-carbon shortening
Thiolytic two-carbon shorteningReactionbacterial_ketoacyl_coa_thiolysis

Releases acetyl-CoA and a shorter acyl-CoA when the selected enzyme/complex accepts that intermediate. C4 thiolysis produces acetyl-CoA as both products and terminates the even-chain cycle.

Variant set: Supported protein implementations by verified family and representative protein [Realizer] (One Or More)
Classical FadA beta-chain thiolysisReactionfada_ketoacyl_coa_thiolase_activity_implementation

Annotons

Classical FadA beta-chain thiolysis
fada_ketoacyl_coa_thiolase_activity
Participant: Family: Classical FadA beta-chain thiolysis
Family:
Classical FadA beta-chain thiolysisPANTHER:PTHR43853:SF11 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadA__Q88L01 (PSEPK)UniProtKB:Q88L01 fadA (ECOLI)UniProtKB:P21151 fadA (SALTY)UniProtKB:P0A2H7 fadA (PSEFR)UniProtKB:P28790

Function

acetyl-CoA C-acyltransferase activityGO:0003988
Substrates: 3-oxoacyl-CoA coenzyme A
Products: acetyl-CoA acyl-CoA shortened by two carbons

Processes

fatty acid beta-oxidationGO:0006635

Operates with the compatible alpha chain. Direct P. fragi reconstitution establishes that an isolated beta dimer is insufficient for detectable activity. LT2/KT2440 pathway genetics do not define isolated beta kinetics or arbitrary cross-species interchangeability.

PMID:9396725
Compatible alpha/beta assembly is required in the P. fragi isolated-subunit assay.
PMID:16385050
LT2 fadBA is exchanged as a pair, so improved processing is not assigned to FadA alone.
file:PSEPK/fadB/fadB-source-analysis/primary-scope.md
Native PP2137 fitness supports a role alongside PP2136 without measuring isolated complex kinetics.
H37Rv FadA thiolysisReactionmycobacterial_fada_thiolase_implementation

Annotons

H37Rv FadA thiolysis
mycobacterial_fada_thiolase
Participant: Family: H37Rv FadA thiolysis
Family:
H37Rv FadA thiolysisPANTHER:PTHR43365:SF1 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadA (MYCTU)UniProtKB:O53871

Function

acetyl-CoA C-acyltransferase activityGO:0003988
Substrates: 3-oxoacyl-CoA coenzyme A
Products: acetyl-CoA acyl-CoA shortened by two carbons

Processes

fatty acid beta-oxidationGO:0006635

Rv0859/O53871 acts in the divergent FadBA complex with Rv0860/O53872. C10/C16 ketoacyl turnover is detected qualitatively; acetoacetyl-CoA activity was not detected under the reported assay. This is not a claim of evolutionary loss, complete shortening through C4, or native sterol-side-chain function.

PMID:23496842
H37Rv TFE has a distinct assembly with exact alpha/beta identities.
file:MYCTU/fadB/fadB-source-analysis/primary-scope.md
Substrate-resolved assays limit what can be inferred about successive cycles.
Bacillus FadA thiolysisReactionbacillus_fada_thiolase_implementation

Annotons

Bacillus FadA thiolysis
bacillus_fada_thiolase
Participant: Family: Bacillus FadA thiolysis
Family:
Bacillus FadA thiolysisPANTHER:PTHR43853:SF21 Representative-backed implementation. Membership alone does not establish the full reaction, substrate range, compatible partners or native pathway flux.
Representative Members: fadA (BACSU)UniProtKB:O32177

Function

acetyl-CoA C-acyltransferase activityGO:0003988
Substrates: 3-oxoacyl-CoA coenzyme A
Products: acetyl-CoA acyl-CoA shortened by two carbons

Processes

fatty acid beta-oxidationGO:0006635

Target genetics and curated thiolase assignment support the step. The official steroid-thiolase subfamily name is preserved and does not establish steroid metabolism, exact chain limits or a purified FadN/FadA assembly.

PMID:17189250
The yusK/fadA perturbation affects native palmitate utilization, distinct from a direct assembly assay.