Bacterial FabA/FabB unsaturated-fatty-acid biosynthesis

A reusable oxygen-independent branch of bacterial type-II fatty-acid synthesis in which FabA dehydrates 3-hydroxydecanoyl-ACP and isomerizes the resulting trans-2-decenoyl-ACP to cis-3-decenoyl-ACP, FabB commits that intermediate to elongation, and FabF can extend palmitoleoyl-ACP toward cis-vaccenoyl-ACP. General FAS-II reduction and dehydration reactions are shared with saturated-fatty-acid synthesis and are outside this focused branch.

MODULE:bacterial_unsaturated_fatty_acid_biosynthesisDRAFTMetabolic Pathwaymodules/bacterial_unsaturated_fatty_acid_biosynthesis.yaml
unsaturated fatty acid biosynthetic processGO:0006636
GO:0006636
unsaturated fatty acid biosynthetic process
GO:0006636 provides the biological-process scope for formation of unsaturated fatty acids.
file:PSEPK/fabA/fabA-uniprot.txt
UniProtKB entry Q88FC4 for PSEPK FabA
The reviewed entry assigns both 3-hydroxydecanoyl-ACP dehydration and trans-2-decenoyl-ACP isomerization to the exact KT2440 FabA exemplar.
file:PSEPK/fabB/fabB-uniprot.txt
UniProtKB entry Q88FC3 for PSEPK FabB
The entry records condensation of cis-3-decenoyl-ACP with malonyl-ACP, the first elongation reaction after FabA introduces cis unsaturation.
file:PSEPK/fabF/fabF-uniprot.txt
UniProtKB entry Q88LL4 for PSEPK FabF
The entry assigns efficient elongation of palmitoleoyl-ACP toward cis-vaccenoyl-ACP to the exact KT2440 FabF exemplar.
UniProtKB:P0A953
Reviewed Escherichia coli FabB UniProt record
The reviewed E. coli FabB record has direct GO evidence for 3-oxoacyl-ACP synthase activity and classifies the protein in PTHR11712:SF306.
UniProtKB:P0A6Q3
Reviewed Escherichia coli FabA UniProt record
The reviewed E. coli FabA record has direct GO evidence for both dehydratase and trans-2-decenoyl-ACP isomerase activities and classifies the protein in PTHR30272:SF8.
UniProtKB:P0AAI5
Reviewed Escherichia coli FabF UniProt record
The reviewed E. coli FabF record has direct GO evidence for 3-oxoacyl-ACP synthase activity and classifies the protein in PTHR11712:SF336.
file:projects/P_PUTIDA/data/psepk_uniprot_metadata.tsv
PSEPK UniProt metadata snapshot
The local UniProt metadata identifies TesA as a multifunctional hydrolase, TesB as an acyl-CoA thioesterase, and PP_5331 as a long-chain acyl-CoA thioester hydrolase; none has an ACP-dependent reaction that introduces or elongates cis unsaturation.
file:modules/bacterial_unsaturated_fatty_acid_biosynthesis-deep-research-openscientist.md
OpenScientist review of bacterial FabA/FabB unsaturated-fatty-acid biosynthesis
Module-level retrieval supports the FabA dehydration/isomerization and FabB commitment boundary, treats FabF extension as conditional, and distinguishes alternative bacterial isomerase routes from this focused module.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_unsaturated_fatty_acid_biosynthesis__ppu01040-deep-research-openscientist.md
OpenScientist PSEPK ppu01040 satisfiability review
Species/pathway retrieval independently identifies the KEGG ppu01040 thioesterase set as outside the ACP-dependent FabA/FabB branch and supports Q88FC4, Q88FC3, and Q88LL4 as the KT2440 pathway implementation.
5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_unsaturated_fatty_acid_biosynthesis-deep-research-openscientist.md (openscientist)

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.

  • fabB_cis_decenoyl_condensation → fabF_palmitoleoyl_condensation [NOT_CHECKED]
    FabB initiates preservation of the cis double bond through iterative FAS-II elongation; after intervening shared cycles produce palmitoleoyl-ACP, FabF can perform the C16:1-to-C18:1 condensation.

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 6 evidence or coverage gap(s) (12 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
fabA_dehydratase PSEPK FabA
UniProtKB:Q88FC4
Family Representative 		(3R)-hydroxyacyl-acyl-carrier-protein dehydratase activity
GO:0019171 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fabA_dehydratase experimentally characterized E. coli FabA
UniProtKB:P0A6Q3
Family Representative 		(3R)-hydroxyacyl-acyl-carrier-protein dehydratase activity
GO:0019171 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
fabA_isomerase PSEPK FabA
UniProtKB:Q88FC4
Family Representative 		trans-2-decenoyl-acyl-carrier-protein isomerase activity
GO:0034017 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fabA_isomerase experimentally characterized E. coli FabA
UniProtKB:P0A6Q3
Family Representative 		trans-2-decenoyl-acyl-carrier-protein isomerase activity
GO:0034017 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
fabB_condensing_enzyme PSEPK FabB
UniProtKB:Q88FC3
Family Representative 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fabB_condensing_enzyme experimentally characterized E. coli FabB
UniProtKB:P0A953
Family Representative 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
fabF_condensing_enzyme PSEPK FabF
UniProtKB:Q88LL4
Family Representative 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fabF_condensing_enzyme experimentally characterized E. coli FabF
UniProtKB:P0AAI5
Family Representative 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
fabA_dehydratase FabA-family dehydratase/isomerases
PANTHER:PTHR30272:SF8
Family 		(3R)-hydroxyacyl-acyl-carrier-protein dehydratase activity
GO:0019171 		Family Supported
Family review supports GO:0019171 FAMILY_WIDE. Asserted by bacterial_unsaturated_fatty_acid_biosynthesis and type_ii_fatty_acid_synthesis; accepted by P. putida FabZ and FabA.
fabA_isomerase FabA-family dehydratase/isomerases
PANTHER:PTHR30272:SF8
Family 		trans-2-decenoyl-acyl-carrier-protein isomerase activity
GO:0034017 		Family Supported
Family review supports GO:0034017 for PANTHER:PTHR30272:SF8. FabA (SF8) only, as both modules select.
fabB_condensing_enzyme FabB/KAS-I condensing enzymes
PANTHER:PTHR11712:SF306
Family 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Family Function Unreviewed
Family review leaves GO:0004315 UNRESOLVED. The inventory includes mitochondrial Cem1, bacterial and plastid fatty-acid ketosynthases, and aromatic polyketide synthase alpha and beta components. Experimental chain-length-factor work separates the noncatalytic beta component from the condensing enzyme (PMID:14558809). Thus even the shared ketosynthase architecture does not confer condensation chemistry on every member. Pombe Cem1 is an SF336 mitochondrial fatty-acid-synthesis comparison, not a polyketide antibiotic assignment.
fabF_condensing_enzyme FabF/KAS-II condensing enzymes
PANTHER:PTHR11712:SF336
Family 		3-oxoacyl-acyl-carrier-protein synthase activity
GO:0004315 		Family Function Unreviewed
Family review leaves GO:0004315 UNRESOLVED. The inventory includes mitochondrial Cem1, bacterial and plastid fatty-acid ketosynthases, and aromatic polyketide synthase alpha and beta components. Experimental chain-length-factor work separates the noncatalytic beta component from the condensing enzyme (PMID:14558809). Thus even the shared ketosynthase architecture does not confer condensation chemistry on every member. Pombe Cem1 is an SF336 mitochondrial fatty-acid-synthesis comparison, not a polyketide antibiotic assignment.

Gene-review completeness (3/6 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 3 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
fabA Q88FC4 ✓ ✓ ✓
fabB Q88FC3 ✓ ✓ ✓
fabF Q88LL4 ✓ ✓ ✓
experimentally characterized E. coli FabA P0A6Q3 ✗ — —
experimentally characterized E. coli FabB P0A953 ✗ — —
experimentally characterized E. coli FabF P0AAI5 ✗ — —

Details

Bacterial FabA/FabB unsaturated-fatty-acid biosynthesisMetabolic Pathwaybacterial_unsaturated_fatty_acid_biosynthesis
unsaturated fatty acid biosynthetic processGO:0006636

Exact KT2440 accessions are representative members and do not restrict the module to Pseudomonas. This oxygen-independent route is often called the anaerobic pathway because it does not require an oxygen-dependent desaturase; that name does not imply that it functions only during anaerobic growth. TesA, TesB, and PP_5331 are excluded because their local records support thioester hydrolysis or other hydrolase activities, not a connected ACP-bound route for introducing cis unsaturation. FabZ and the remaining reductive FAS-II enzymes are shared-cycle context rather than defining members of this focused branch. This module is authoritative for the FabA dehydration/isomerization, FabB commitment, and optional FabF extension reactions. The broader type_ii_fatty_acid_synthesis module retains a compact copy of the FabA/FabB branch only to show where it diverges from the shared elongation cycle. PANTHER's official PTHR11712:SF336 label includes "MITOCHONDRIAL" even though the subfamily also contains bacterial FabF proteins; the label is retained verbatim for identifier validation and is not a localization assertion for this module.

Connections

The first FabA reaction supplies trans-2-decenoyl-ACP.
FabA supplies cis-3-decenoyl-ACP to FabB.
Part 1: decanoyl-branch dehydration
FabA 3-hydroxydecanoyl-ACP dehydrationReactionfabA_hydroxydecanoyl_dehydration

Annotons

FabA 3-hydroxydecanoyl-ACP dehydratase
fabA_dehydratase
Participant: Family: FabA-family dehydratase/isomerases
Family:
FabA-family dehydratase/isomerasesPANTHER:PTHR30272:SF8
Representative Members: PSEPK FabAUniProtKB:Q88FC4 experimentally characterized E. coli FabAUniProtKB:P0A6Q3

Function

(3R)-hydroxyacyl-acyl-carrier-protein dehydratase activityGO:0019171
Substrates: (3R)-hydroxydecanoyl-ACP
Products: trans-2-decenoyl-ACP water

Generates the trans-2-decenoyl-ACP substrate for the double-bond-shifting FabA reaction.

Part 2: cis double-bond introduction
FabA trans-2-decenoyl-ACP isomerizationReactionfabA_decenoyl_isomerization

Annotons

FabA trans-2-decenoyl-ACP isomerase
fabA_isomerase
Participant: Family: FabA-family dehydratase/isomerases
Family:
FabA-family dehydratase/isomerasesPANTHER:PTHR30272:SF8
Representative Members: PSEPK FabAUniProtKB:Q88FC4 experimentally characterized E. coli FabAUniProtKB:P0A6Q3

Function

trans-2-decenoyl-acyl-carrier-protein isomerase activityGO:0034017
Substrates: trans-2-decenoyl-ACP
Products: cis-3-decenoyl-ACP

Introduces the cis double bond at the committed branch point.

Part 3: committed unsaturated-chain elongation
FabB cis-3-decenoyl-ACP condensationReactionfabB_cis_decenoyl_condensation

Annotons

FabB 3-oxoacyl-ACP synthase I
fabB_condensing_enzyme
Participant: Family: FabB/KAS-I condensing enzymes
Family:
FabB/KAS-I condensing enzymesPANTHER:PTHR11712:SF306
Representative Members: PSEPK FabBUniProtKB:Q88FC3 experimentally characterized E. coli FabBUniProtKB:P0A953

Function

3-oxoacyl-acyl-carrier-protein synthase activityGO:0004315
Substrates: cis-3-decenoyl-ACP malonyl-ACP
Products: 3-oxo-cis-5-dodecenoyl-ACP holo-ACP carbon dioxide

Commits the FabA product to elongation while retaining the cis double bond.

Part 4: long-chain unsaturated-product extension (optional)
FabF palmitoleoyl-ACP condensationReactionfabF_palmitoleoyl_condensation

Annotons

FabF 3-oxoacyl-ACP synthase II
fabF_condensing_enzyme
Participant: Family: FabF/KAS-II condensing enzymes
Family:
FabF/KAS-II condensing enzymesPANTHER:PTHR11712:SF336
Representative Members: PSEPK FabFUniProtKB:Q88LL4 experimentally characterized E. coli FabFUniProtKB:P0AAI5

Function

3-oxoacyl-acyl-carrier-protein synthase activityGO:0004315
Substrates: cis-9-hexadecenoyl-ACP malonyl-ACP
Products: 3-oxo-cis-11-octadecenoyl-ACP holo-ACP carbon dioxide

Extends palmitoleoyl-ACP into the cis-vaccenoyl branch; shared FAS-II reduction reactions complete the elongation round.