Bacterial fatty acid beta-oxidation spiral

A reusable bacterial four-reaction spiral that shortens a fatty acyl-CoA by two carbon atoms per turn. An acyl-CoA dehydrogenase forms a trans-2-enoyl-CoA, an enoyl-CoA hydratase forms a (3S)-3-hydroxyacyl-CoA, a hydroxyacyl-CoA dehydrogenase forms a 3-oxoacyl-CoA, and a thiolase releases acetyl-CoA plus a chain-shortened acyl-CoA that re-enters the first reaction. Bacterial pathway architecture can use separate enzymes or a multifunctional FadBA complex; free-fatty-acid activation and unsaturated-fatty-acid auxiliary reactions are outside the core spiral.

The module is species-neutral and uses Pseudomonas putida KT2440 as a bacterial realization. FadD-dependent ligation of free fatty acids to CoA is an optional entry process, not a spiral reaction. Enoyl-CoA isomerases, 2,4-dienoyl-CoA reductases, and related enzymes required for unsaturated substrates are auxiliary. Alkane oxidation, phenylacetate degradation, glutaryl-CoA oxidation, PHA metabolism, transport, and specialty acyl-CoA pathways are separate modules. Molecular functions and exact chemistry are asserted only on leaf annotons; no generic cytoplasmic location is asserted at module level.