Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the fifth step of the pathway, the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDPG). 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + H(+) Belongs to the carbohydrate kinase PfkB family.