Overview of the daily cellular metabolism in Cyanothece ATCC51142. The biochemical pathways were predicted based on the current data and the available information in the literatures [11–13, 16, 39, 52, 60–62]. Each arrow shows the direction of the reaction. Boxed numbers denote individual or group of enzymes involved for various biochemical reactions, and color indicate whether the protein or majority of the proteins in the group have higher expression in the light (red) or in the dark (blue). The RIA values of these proteins can be found in Additional file 1, Table S2. 1, beta-carbonic anhydrase (IcfA1); 2, CO2 concentrating mechanism proteins (CcmM, CcmK2, CcmK4); 3, ribulose 1, 5-bisphosphate carboxylase oxygenase (RbcL); 4, glycogen synthase (GlgA1); 5, 1, 4-glucan debranching enzyme (GlgB1, GlgB2); 6, glycogen phosphorylase (GlgP1); 7, glucose-6-phosphate dehydrogenase (Zwf); 8, enzymes of glycolysis (Fba, Gap, Eno, Pgk, PykF1); 9, enzymes of pentose phosphate pathway (OpcA, TktA, TalA, Gnd, Pgl); 10, pyruvate dehydrogenase (PdhA, PdhC, IpdA); 11, citrate synthase (GltA); 12, enzymes of TCA cycle (AcnB, Icd, GabD, Mdh, SucC); 13, glutamine synthetase (GlnA); 14, glutamate synthase (GlsF); 15, nitrogenase (NifHDK); 16, nitrogenase co-factor biosynthesis (NifB, NifS); 17, respiratory enzymes (CobB1, PetH); 18, carbamoyl-phosphate synthase (CarB); 19, ornithine carbamoyltransferase (ArgF); 20, argininosuccinate synthetase (ArgG); 21, chorismate synthase (AroC); 22, S-adenosylmethionine synthetase (metK); 23, Fe-S cluster biosynthesis proteins (HesB), 24, cyanophycin synthetase; (CphA), 25, cyanophycinase (CphB); 26, enzymes of fatty acid/phospholipid metabolism; 27, enzymes of nucleotides metabolism; 28, co-factor biosynthesis enzymes; 29, PSII proteins; 30, cytochrome b6f complex (PetA, PetB, PetD); 31, PSI proteins; ATP synthase; 32, enzymes of stress and redox regulation. PSI, photosystem I; PSII, photosystem II; Qb, plastoquinone Qb; Cytb6f, cytochrome b6f complex; PC, plastocyanin; FNR, ferredoxin NADP reductase; ATPase, ATP synthase; 3-PGA, 3-phosphoglycerate; 2-OG, 2-oxoglutarate; Gln, glutamine; Glu, glutamate.