Table 4 Selected genes and gene clusters in metabolic pathways of Cfl. aurantiacus

CO oxidation

coxSML and coxG (Caur_3467 - 3470)

CO₂-anaplerotic pathways

tme (Caur_1614), pckA (Caur_2331), ppc (Caur_3161, Caur_3888)

3-hydroxypropionate cycle

accC (Caur_1378, Caur_3421), accA (Caur_1647), accD (Caur_1648), accB (Caur_3739), mcr (Caur_2614), pcs (Caur_ 0613), pccB (Caur_2034, Caur_3435), mcee (Caur_3037), mut (Caur_1844, Caur_2508, Caur_2509), smtA (Caur_0179), smtB (Caur_0178), sdhBAC (Caur_1880 to Caur_1882), fh (Caur_1443), mcl (Caur_0174), mch (Caur_0173), mct (Caur_0174), meh (Caur_0180)

Glycolate assimilation and glyoxylate cycle

glcDEF (Caur_1144 - 1145, Caur_2133, Caur_2135), glyr (Caur_0825), icl (Caur_3889) and mas (Caur_2969)

Cobalamin biosynthesis

cobS (Caur_1198), cobQ/cbiP (Caur_2560), N-transferase (Caur_2561), cobP/cobU (Caur_2562), cobB/cbiA (Caur_2563), cobA (Caur_2564, Caur_0687), cobJ (Caur_2565), cobM/cbiF (Caur_2566), cobI/cbiL (Caur_2567), cobL/cbiET (Caur_2568), cbiD (Caur_2569), cobH/cbiCH (Caur_2570), cbiK (Caur_2572), cobD/cbiB (Caur_2573), cbiMNQO (Caur_2574 to Caur_2577), cobU/cobT (Caur_2578), cobN (Caur_2579), cobO (Caur_2580), cysG (Caur_0688) and cbiMNQ (Caur_3680 to Caur_3682) (Genes shared with aerobic and anaerobic pathways shown as aerobic/anaerobic)

Heme biosynthesis

hemA, hemC, hemD, hemB, hemE, hemL, hemF (Caur_2593 - 2599), hemN (Caur_0209 and Caur_0644), hemG/Y (Caur_0645), protoheme IX farnesyltransferase (Caur_0029)

Chlorophyll biosynthesis

bchI (Caur_0117, Caur_0419, Caur_1255), bchU (Caur_0137), bchK (Caur_0138), bchF (Caur_0415), bchC (Caur_0416), bchX (Caur_0417), bchD (Caur_0420), bchP (Caur_2087), bchG (Caur_2088), bchBNL (Caur_2554 to Caur_2557), bchM (Caur_2588), acsF (Caur_2590), bchH (Caur_2591, Caur_3151, Caur_3371), bchE (Caur_3676), bchJ (Caur_3677), and bchYZ (Caur_3805, Caur_3806)

Nitrogen metabolism and amino acid biosynthesis

hal (Caur_0974), tpl (Caur_0573), aspg (Caur_3511), glud 1 (Caur_1698, Caur_2070), glul (Caur_0844, Caur_1448, Caur_3395), ilvA (Caur_2585, Caur_3892), isoleucine/leucine/valine biosynthesis (Caur_0041, Caur_0163 - 0169, Caur_0329 - 0331, Caur_0488, Caur_1435, and Caur_2851)

Sulfur metabolism

Sulfur reduction operon (Caur_0686 - 0692), a sulfate adenylyl-transferase/adenylylsulfate kinase (Caur_2113), cysK (Caur_1341), cysM (Caur_3489), sqr (Caur_3894, type II SQR), sulfotransferase (Caur_2114).

B808-866 light-harvesting complex

Caur_2090 (α-subunit) and Caur_2091 (β-subunit)

Reaction center

pufM (Caur_1051) and pufL (Caur_1052)

Chlorosome proteins

csmA (Caur_0126), csmM (Caur_0139), csmN (Caur_0140), csmP (Caur_0142), csmO (Caur_1311) and csmY (Caur_0356).

Auracyanins (type I blue-copper proteins)

auraA (Caur_3248), auraB (Caur_1950), Caur_2212 and Caur_2581

Cytochrome c₅₅₄ complex

pufC (Caur_2089)

Succinate dehydrogenase/fumarate reductase (complex II, EC 1.3.99.1)

sdhBAC (Caur_1880 - 1882)

Cytochrome bc ₁ or b ₆ /f complex

Not annotated

Cytochrome c oxidase (complex IV, EC 1.9.3.1)

COX I - IV (Caur_2141 - 2144), COX I (Caur_2426) and COX II (Caur_2425 and Caur_2582)