Bacterial glycolate and glyoxylate assimilation

A reusable bacterial central-carbon module for conversion of glycolate and glyoxylate into metabolites that can re-enter core carbon metabolism. The core module starts at glycolate oxidation to glyoxylate and continues through the glyoxylate carboligase/tartronate-semialdehyde branch that converts glyoxylate-derived carbon toward glycerate. Optional glycolate-source routes, including phosphoglycolate salvage, can feed this core but are not required in every organism. Pseudomonas putida KT2440 provides local exemplars for GlcDEF glycolate dehydrogenase, Gcl, Hyi, and GlxR; PP_0416/PP_1907 remain housekeeping phosphoglycolate-salvage candidates rather than the physiological ppu00630 entry route.

PSEPK interpretation after species-aware review: GlcDEF, Gcl, Hyi, and GlxR form the physiologically relevant glycolate-to-glycerate module core. PP_0416, PP_1907, and PP_0094 may be phosphoglycolate/small-phosphometabolite salvage enzymes, but they should not be counted as the physiological glycolate-entry route for KT2440 ppu00630 because KT2440 lacks the CBB/photorespiratory context that makes 2-phosphoglycolate a major glycolate source. The Gcl/Hyi/ GlxR branch is genetically present but conditionally active because the branch is repressed in wild-type KT2440 and derepressed in ethylene-glycol-adapted contexts. This module deliberately excludes the broader KEGG ppu00630 spillover into catalase, formate dehydrogenase, glycine cleavage, one-carbon folate, TCA, glyoxylate shunt, and downstream glycerate kinase reactions. AceA/GlcB glyoxylate-shunt logic should remain in a separate glyoxylate-bypass module.