Table 2.
Coverage of kinetic rates obtained from the databases with (+) and without (-) the use of identifier translators
| Model | Database | k M | k cat | k eq | |||
|---|---|---|---|---|---|---|---|
| + | - | + | - | + | - | ||
| E. coli | # rates | 10183 | 2583 | 2583 | |||
| iJO1366 | BRENDA | 637 | 591 | 286 | 259 | / | / |
| eQuilibrator | / | / | / | / | 491 | 0 | |
| SABIO-RK | 228 | 0 | 4 | 0 | 0 | 0 | |
| # found | 700 | 591 | 290 | 259 | 491 | 0 | |
| E. coli | # rates | 380 | 95 | 95 | |||
| Core model | BRENDA | 29 | 0 | 10 | 0 | / | / |
| eQuilibrator | / | / | / | / | 37 | 0 | |
| SABIO-RK | 10 | 0 | 2 | 0 | 0 | 0 | |
| # found | 33 | 0 | 12 | 0 | 37 | 0 | |
| S. cerevisiae | # rates | 5509 | 1612 | 1612 | |||
| iTO977 | BRENDA | 342 | 330 | 113 | 108 | / | / |
| eQuilibrator | / | / | / | / | 450 | 0 | |
| SABIO-RK | 104 | 96 | 3 | 0 | 0 | 0 | |
| # found | 370 | 356 | 116 | 108 | 450 | 0 | |
| L. lactis | # rates | 73 | 21 | 21 | |||
| BRENDA | 2 | 2 | 1 | 1 | / | / | |
| eQuilibrator | / | / | / | / | 12 | 0 | |
| SABIO-RK | 2 | 2 | 0 | 0 | 0 | 0 | |
| # found | 3 | 3 | 1 | 1 | 12 | 0 |
Rhea, MetaCyc and MetaNetX databases were used for identifier translation
If multiple values were found for the same reaction rate then this was only counted once
If the rate is not available from this database, it is noted with /