Table I. Comparison of different metabolic pathway gene databases.
Genes annotated as isoprenoid pathway genes in the BioPathAt database were extracted from BioPathAtDB_Oct2004.zip (http://www.ibc.wsu.edu/research/lange/public_folder/BioPathAt_V1_Oct2004/) and from Lange and Ghassemian (2003). AraCyc isoprenoid pathway genes were extracted from the AraCyc pathway database (AraCyc version 7.0; http://www.arabidopsis.org/biocyc/downloads.jsp). KEGG isoprenoid pathway genes were extracted from the KEGG PATHWAY maps (http://www.genome.jp/kegg/pathway.html).
| Pathway | No. of Genes |
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| BioPathAt | AraCyc | KEGG | AtIPD | |
| Mevalonic acid pathway | 9 | 7 | 8 | 9 |
| Prenyl diphosphate biosynthesis | 27 | 20 | 30 | 31 |
| Sterol biosynthesis | 20 | 22 | 19 | 25 |
| Brassinosteroid biosynthesis | 3 | 6 | 6 | 8 |
| Triterpenoid biosynthesis | 11 | 14 | 4 | 14 |
| Sesquiterpenoid biosynthesis | 16 | 3 | 0 | 16 |
| Diterpenoid biosynthesis | 19 | 0 | 0 | 19 |
| Protein prenylation | 7 | 2 | 0 | 7 |
| Cytokinin biosynthesis and catabolism | 0 | 17 | 17 | 25 |
| Ubiquinone biosynthesis | 4 | 2 | 4 | 4 |
| 2-C-Methyl-d-erythritol 4-phosphate pathway | 7 | 6 | 7 | 7 |
| Chlorophyll biosynthesis and catabolism | 29 | 35 | 30 | 37 |
| Carotenoid biosynthesis | 11 | 13 | 11 | 15 |
| Apocarotenoid biosynthesis | 0 | 2 | 0 | 5 |
| Abscisic acid biosynthesis and catabolism | 1 | 12 | 11 | 12 |
| Plastoquinone, plastochromanol, tocopherol biosynthesis | 5 | 7 | 7 | 7 |
| Phylloquinone biosynthesis | 7 | 9 | 5 | 9 |
| GA biosynthesis and catabolism | 16 | 22 | 15 | 23 |
| Monoterpenoid biosynthesis | 5 | 6 | 4 | 6 |
| Total | 197 | 205 | 178 | 279 |