Table 1.
Genome-wide enzyme identification for three bacterial genomes (E. coli, B. aphidicola, and M. pneumoniae) and one eukaryotic genome (P. falciparum) by ModEnzA and EFICAz.
| Methods | EFICAz | ModEnzA(Tier I) | ModEnzA(Tier I+II) | |
|---|---|---|---|---|
| Annotation benchmark | HAMAP | |||
|
| ||||
| E. coli | ||||
| Sequences | 1012 | 859 (1051) | 902 (1021) | 930 (1082) |
| Sensitivity | 84.88 | 89.13 | 91.89 | |
| Specificity | 81.73 | 88.34 | 85.95 | |
| EC numbers | 755 | 653 (728) | 663 (697) | 699 (775) |
| Sensitivity | 86.49 | 87.81 | 92.58 | |
| Specificity | 89.69 | 95.12 | 90.19 | |
| B. aphidicola | ||||
| Sequences | 273 | 257 (273) | 264 (271) | 265 (273) |
| Sensitivity | 94.13 | 96.7 | 97.07 | |
| Specificity | 94.13 | 97.41 | 97.07 | |
| EC numbers | 245 | 226 (238) | 225 (229) | 225 (233) |
| Sensitivity | 92.24 | 91.83 | 91.83 | |
| Specificity | 94.95 | 98.25 | 96.56 | |
| M. pneumoniae | ||||
| Sequences | 147 | 119 (149) | 126 (139) | 126 (139) |
| Sensitivity | 80.95 | 85.71 | 85.71 | |
| Specificity | 79.86 | 90.64 | 90.64 | |
| EC numbers | 127 | 101 (122) | 115 (122) | 115 (122) |
| Sensitivity | 79.52 | 90.55 | 90.55 | |
| Specificity | 82.78 | 94.26 | 94.26 | |
|
| ||||
| Annotation benchmark | PlasmoDB | |||
|
| ||||
| P. falciparum | ||||
| Sequences | 771 | 341 (480) | 350 (415) | 358 (431) |
| Sensitivity | 44.22 | 45.39 | 46.43 | |
| Specificity | 71.04 | 84.33 | 83.06 | |
| EC numbers | 410 | 217 (247) | 212 (234) | 215 (242) |
| Sensitivity | 52.92 | 51.7 | 52.43 | |
| Specificity | 87.85 | 90.59 | 88.84 | |
Numbers within parentheses indicate the total number of sequences or EC numbers identified by each method.