Table 2 Statistical characteristics of improved annotation and metabolic reconstruction.
From: Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
Characteristics of improved annotation | Improved annotated data | Database |
|---|---|---|
Total protein-encoding genes | 13,120 | 12,074 |
New putative protein functions to newly predicted genes | 398 | - |
   Metabolic functions | 154 | - |
   Other functional groups | 244 | - |
Hypothetical proteins to newly predicted genes | 648 | - |
New putative protein functions to previously hypothetical proteins | 1,469 | - |
   Metabolic functions | 562 | - |
   Other functional groups | 907 | - |
Same putative protein functions | 5,391 | 5,391 |
   Metabolic functions | 3,178 | 3,178 |
   Other functional groups | 2,213 | 2,213 |
Hypothetical proteins | 5,214 | 6,683 |
Characteristics of network | A. oryzae | A. nidulans |
Enzymes-encoding genes | 1,314 | 666 |
Enzymes | 729 | 466 |
Metabolites | 1,073 | 733 |
Biochemical reactions | 1,846 (1,053 Unique) | 1,090 (676 Unique) |
   Cytosol | 832 | 551 |
   Mtochondria | 172 | 103 |
   Glyoxysome | - | 5 |
   Peroxisome | 19 | - |
   Extracellular | 30 | 17 |
Transport reactions | 281 (161 Unique) | 118 (113 Unique) |
   Reactions with gene assignments | 173 (53 Unique) | 15 (12 Unique) |
   Reactions without gene assignments | 108 (108 Unique) | 103 (101 Unique) |