Catalyzes the formation of 2-keto-3-deoxy-gluconate (KDG) from pyruvate and glyceraldehyde (PubMed:21294156). May also function as a 2-dehydro-3-deoxy-D-pentonate aldolase (PubMed:23233208). Overexpression leads to increased growth (over 2 hours) in the presence of the antibiotics norfloxacin, ampicillin and streptomycin (PubMed:21294156). 2-dehydro-3-deoxy-D-gluconate = D-glyceraldehyde + pyruvate 2-dehydro-3-deoxy-D-arabinonate = glycolaldehyde + pyruvate A dimer of dimers. Expression is repressed by the transcriptional regulator XynR. Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhH-yagE double mutant cannot use D-xylonate as the sole source of carbon. Part of prophage CP4-6. Belongs to the DapA family. Extended N-terminus.