Table 3 Analysis of Subsystems at level 3. From the 28 subsystems at level 3 registered by MG-RAST, only those subsystems with more than 2000 reads assigned were collected in the table.
SEED subsystems | No. of reads | |||
|---|---|---|---|---|
Level 1 | Level 2 | Level 3 | BW1 | BW2 |
Amino acids and derivatives | Branched-chain amino acids | branched-chain_amino_acid_biosynthesis | 2799 | 2930 |
Lysine, threonine, methionine, and cysteine | methionine_biosynthesis | 3119 | 3134 | |
Carbohydrates | CO2 fixation | Calvin-benson_cycle | 2204 | 2351 |
One-carbon Metabolism | Serine-glyoxylate_cycle | 3311 | 3219 | |
Cell Wall and capsule | NULL | Peptidoglycan_biosynthesis | 2039 | 2106 |
Clustering-based subsystems | NULL | Bacterial_cell_division | 2293 | 2119 |
Cofactors, vitamins, prosthetic groups, pigments | Tetrapyrroles | Heme_and_siroheme_biosynthesis | 2244 | 2205 |
Folate and pterines | YgfZ | 2527 | 2741 | |
DNA metabolism | DNA replication | DNA-replication | 2446 | 2332 |
DNA repair | DNA_repair,_UvrABC_system | 2038 | 2019 | |
DNA repair | DNA_repair,_bacterial | 2532 | 2661 | |
Fatty acids, lipids, and isoprenoids | Fatty acids | Fatty_Acid_biosynthesis_FASII | 2365 | 2459 |
Membrane transport | ABC transporters | ABC_transporter_branched-chain_amino_acid_(TC_3.A.1.4.1) | 2598 | 2380 |
Motility and chemotaxis | Flagellar motility in prokaryota | Flagellum | 3061 | 2874 |
Nitrogen metabolism | NULL | Ammonia_assimilation | 2028 | 2279 |
NULL | Nitrate_and_nitrite_ammonification | 4965 | 4169 | |
Nucleosides and nucleotides | Purines | De_novo_purine_biosynthesis | 2868 | 3365 |
Purines | Purine_conversions | 2695 | 2672 | |
Phosphorus metabolism | NULL | Phosphate_metabolism | 3204 | 3396 |
Protein metabolism | Protein folding | Protein_chaperones | 2584 | 2551 |
Protein degradation | Proteolysis_in_bacteria,_ATP-dependent | 2054 | 1933 | |
Protein biosynthesis | Ribosome_LSU_bacterial | 4896 | 4258 | |
Protein biosynthesis | Ribosome_SSU_bacterial | 3084 | 2958 | |
Protein biosynthesis | Universal_GTPases | 2110 | 2012 | |
Respiration | Electron donating reactions | Respiratory_complex_I | 5524 | 5578 |
Electron accepting reactions | Terminal_cytochrome_C_oxidases | 3054 | 2826 | |
RNA metabolism | Transcription | RNA_polymerase_bacterial | 3475 | 3402 |
RNA processing and modification | tRNA_modification_archaea | 1801 | 2035 | |
Sulfur metabolism | NULL | Sulfur_oxidation | 3112 | 2665 |
