## 3 Results
### Gene Clusters and Pathway Associated with Lutein and Zexanthin Biosynthesis  
Lutein and zeaxanthin contain two ionone rings in its chemical formula. They are carotenoids. Carbon fixation pathways in prokaryotes and glycolysis and gluconeogenesis are believed to be involved in the synthesis of lutein and zeaxanthin (Figure S2). These genes, _ackA_, _pgm_, _gpml_, and _pckA_, are unique in _Sphingomonas morindae_ sp. NBD5 (Table 2). _gpml_ encodes a cofactor independent phosphoglycerate mutase that catalyzes the conversion of glycerate-3-phosphate to glycerate-2-phosphate. It involves in glycolysis/glucoseogenesis to generate glyceraldehyde 3-phosphate and pyruvate, providing a carbon skeleton for MP biosynthesis. _pckA_ encodes a phosphoenolpyruvate carboxykinase, which catalyzes the conversion of oxaloacetate to phosphoenol-pyruvate. It participates to  
Figure 2: Distributions of second level GO of _Sphingomonas morindae_ sp. NBD5 genome sequence. The _y_-axis indicates the GO ontology; the _x_-axis represents the number of unigenes in a category. generate pyruvate in the glycolysis/gluconeogenesis pathway, providing a carbon skeleton for MP biosynthesis. _pgm_ encodes a phosphoglucomutase directly involved in the glycolysis/gluconeogenesis pathway. It catalyzes \(\alpha\)-D-glucose 1-phosphate into \(\alpha\)-D-glucose 6-phosphate, which provides a carbon skeleton for MP biosynthesis. _ackA_ encodes an acetate kinase that catalyzes the conversion of acetate to acetyl phosphate. It involves in the glycolysis/gluconeogenesis pathway, and the negative feedback regulates the process of pyruvate to acetyl CoA (Figure S3). The genes _pckG_, _porB_, _meh_, and _fldA_ are characteristic in _Sphingopyris_ sp. USTB-05 (Table 2). _pckG_ encodes phosphoenolpyruvate carboxykinase, which catalyzes the conversion of oxaloacetate to phosphoenol-pyruvate. It directly participates in the glycolysis/gluconeogenesis pathway to generate pyruvate and provide a carbon skeleton for MP biosynthesis. _porB_ encodes 2-oxoglutarate ferredoxin oxidoreductase-tase, which catalyzes the conversion of succinyl-CoA to 2-oxoglutarate in carbon fixation pathways. _meh_ encodes 3-methylfumaryl-CoA hydratase, which catalyzes the conversion of 3-methylfumaryl-CoA to (3S)-citramally-CoA in the carbon fixation pathways in prokaryotes. _fldA_ encodes 2-methylfumaryl-CoA isomerase, which catalyzes the conversion of 2-methylfumaryl-CoA to 3-methylfumaryl-CoA in the carbon fixation pathways. _pgm_ exists in the NBD5 strain and encodes phosphoglucomutase, which catalyzes \(\alpha\)-D-glucose 1-phosphate into \(\alpha\)-D-glucose 6-phosphate. No gene encoding phosphoglucomutase was found in USTB-05 strain. \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Pathway** & **Genes** & **Coded Protein/Enzyme** & **Catalytic Substrate** & **Catalytic Product** \\ \hline Glycolysis\&Glucone- & _pgm_* & Phosphoglucomutase & \(\alpha\)-D-glucose 1-phosphate & \(\alpha\)-D-glucose 6-phosphate \\  & _glk_ & Glucokinase & \(\alpha\)-D-glucose & \(\alpha\)-D-glucose 6-phosphate \\  & _gallM_ & Aldose 1-epimerase & \(\alpha\)-D-glucose & \(\beta\)-D-glucose \\  & _pgi_ & Glucose-6-phosphate isomerase & \(\beta\)-D-glucose 6-phosphate & \(\beta\)-D-fructose 6-phosphate \\ Glycolysis\&Glucone- & _ftp_ & Fructose bisphosphatase & \(\beta\)-D-fructose 6-phosphate & \(\beta\)-D-fructose 1,6-bisphosphate \\ genesis & _fbuB_ & Phosphoglycerate kinase & \(\beta\)-D-fructose 1,6-bisphosphate & Glyceraldehyde-3-phosphate \\  & _tpiA_ & Phosphotriose isomerase & Glycerone-phosphate & Glyceraldehyde-3-phosphate \\  & _gapA_ & Glyceraldehyde-3-phosphate & Glyceraldehyde-3-phosphate \\  & _pgk_ & Phosphoglycerate kinase & Glycerate-1,3-bisphosphate & Glycerate-3-phosphate \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Genes related to macular pigment biosynthesis in _Spingomonas morindae_ sp. NBD5 and _Sphingopyris_ sp. USTB-05. Figure 3: COG functional classification of _Sphingomonas morindae_ sp. NBD5. The columns represent the number of unigenes in each subcategory.