Table 4 Check for all 54 enzymes not found in KEGG or SWISS-PROT. All of the 54 enzymes that were not found in E. coli specific entries of KEGG PATHWAY or SWISS-PROT database were manually checked with EcoCyc and iJR904. Although there were 6 probable mis-annotations by the GEM System, most enzymes were correctly identified in EcoCyc. This is mostly due to the inconsistencies of EC numbers among databases.
From: GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
GEM | gene name | EcoCyc | KEGG(ECOLI) | Swissprot(ECOLI) | iJR904 | description |
|---|---|---|---|---|---|---|
1.10.2.- | cyoA-D, appB-C | 1.10.2.- | 1.10.3.- | 1.10.3.- | no EC | inconsistency of EC (incomplete EC) |
1.14.3.- | ubiH | 1.14.3.- | 1.14.13.- | 1.14.13.- | N.A. | inconsistency of EC (incomplete EC) |
1.16.1.- | ndh | 1.16.1.- | 1.6.99.3 | 1.6.99.3 | N.A. | inconsistency of EC (incomplete EC) |
1.17.4.- | nrdA-B, E-F | 1.17.4.-, 1.17.4.1 | 1.17.4.1 | 1.17.4.1 | N.A. | inconsistency of EC (incomplete EC) |
1.18.99.1 | hyfA-F, H | no EC | 1.-.-.- | 1.-.-.- | N.A. | possible misannotation by GEM System (EC not applicable) |
1.2.1.19 | feaB | 1.2.1.39 | 1.2.1.39 | 1.2.1.39 | 1.2.1.39 | missannotation by GEM System |
1.2.1.21 | aldA | 1.2.1.21 | 1.2.1.21, 1.2.1.22 | 1.2.1.21, 1.2.1.22 | 1.2.1.21 | KEGG PATHWAY mainly uses 1.2.1.22 |
1.2.1.24 | feaB | 1.2.1.39 | 1.2.1.39 | 1.2.1.39 | 1.2.1.39 | missannotation by GEM System |
1.3.-.- | frdD | 1.3.5.- | 1.3.99.1 | N.A. | 1.3.99.1 | inconsistency of EC (incomplete EC) |
1.3.1.10 | fabI | 1.3.1.9, 1.3.1.10 | 1.3.1.9 | 1.3.1.9 | N.A. | 1.3.1.10 specifically functions as 1.3.1.9 in E.coli |
1.4.3.- | nadB | 1.4.3.- | 1.4.3.16 | 1.4.3.16 | N.A. | inconsistency of EC (incomplete EC) |
1.5.3.2 | solA | 1.5.3.2 | 1.5.3.1 | 1.5.3.- | N.A. | inconsistency of EC |
1.6.4.2 | gor | 1.8.1.7 | 1.8.1.7 | 1.8.1.7 | N.A. | inconsistency of EC (1.6.4.2 is changed to 1.8.1.7) |
1.6.4.5 | trxB | 1.6.4.5 | 1.8.1.9 | 1.8.1.9 | 1.6.4.5 | inconsistency of EC (1.6.4.5 is changed to 1.8.1.9) |
1.6.6.- | nirB | 1.7.1.4 | 1.7.1.4 | 1.7.1.4 | no EC | inconsistency of EC (1.6.6.4 is changed to 1.7.1.4) |
1.6.6.8 | guaC | 1.6.6.8 | 1.7.1.7 | 1.7.1.7 | 1.6.6.8 | inconsistency of EC (1.6.6.8 is changed to 1.7.1.7) |
1.6.8.1 | cysI-J | 1.6.8.1, 1.8.1.2 | 1.8.1.2 | 1.8.1.2 | N.A. | inconsistency of EC |
2.3.1.38 | fabH | 2.3.1.-, 2.3.1.38 | 2.3.1.41 | 2.3.1.41 | 2.3.1.38 | inconsistency of EC |
2.3.1.40 | aas | 2.3.1.40, 6.2.1.20 | 2.3.1.40, 6.2.1.20 | 2.3.1.40, 6.2.1.20 | 6.2.1.20 | inconsistency of EC |
2.4.2.15 | deoD | 2.4.2.-, 2.4.2.15, 2.4.2.1 | 2.4.2.1 | 2.4.2.1 | 2.4.2.1 | inconsistency of EC |
2.5.1.1 | ispA | 2.5.1.1, 2.5.1.10 | 2.5.1.10 | 2.5.1.10 | 2.5.1.1, 2.5.1.10 | inconsistency of EC |
2.6.-.- | serC | 2.6.-.-, 2.6.1.52 | 2.6.1.52 | 2.6.1.52 | 2.6.1.52 | inconsistency of EC (incomplete EC) |
2.6.1.29 | ygjG | 2.6.1.29 | 2.6.1.13 | 2.6.1.13 | 2.6.1.13 | inconsistency of EC |
3.1.3.6 | cpdB | 3.1.3.6 | 3.1.4.16 | 3.1.4.16 | N.A. | inconsistency of EC |
3.1.3.8 | agp | 3.1.3.8, 3.1.3.10 | 3.1.3.10 | 3.1.3.10 | 3.1.3.10 | inconsistency of EC |
3.5.1.44 | cheB | 3.5.1.-, 3.1.1.-, 3.1.1.61, 3.5.1.44 | 3.1.1.61 | 3.1.1.61 | N.A. | inconsistency of EC |
3.5.4.- | tadA | 3.5.4.- | N.A. | 3.5.4.- | N.A. | not available in KEGG PATHWAY (incomplete EC) |
3.6.1.34 | atpA-G | 3.6.1.34 | 3.6.3.14 | 3.6.3.14 | 3.6.3.14 | inconsistency of EC (3.6.1.34 is changed to 3.6.3.14) |
4.1.1.3 | eda | 4.1.1.3, 4.1.2.14, 4.1.3.16 | 4.1.2.14, 4.1.3.16 | 4.1.2.14, 4.1.3.16 | 4.1.2.14 | inconsistency of EC |
4.1.2.15 | aroF-H | 4.1.2.15 | 2.5.1.54 | 2.5.1.54 | 4.1.2.15 | inconsistency of EC (4.1.2.15 is changed to 2.5.1.54) |
4.1.2.16 | kdsA | 4.1.2.16 | 2.5.1.55 | 2.5.1.55 | 4.1.2.16 | inconsistency of EC (4.1.2.16 is changed to 2.5.1.55) |
4.1.2.40 | ydjI | N.A. | N.A. | N.A. | N.A. | possible misannotation by GEM System by sequence similarity to |
4.1.3.12 | leuA | 4.1.3.12 | 2.3.3.13 | 2.3.3.13 | 4.1.3.12 | inconsistency of EC (4.1.3.12 is changed to 2.3.3.13) |
4.1.3.18 | ilvB, G-I, M-N | 2.2.1.6, 4.1.1.71 | 2.2.1.6 | 2.2.1.6 | 4.1.3.18 | inconsistency of EC (4.1.3.18 is changed to 2.2.1.6) |
4.1.3.27 | trpD | 2.4.2.18, 4.1.3.27 | 2.4.2.18, 4.1.3.27 | 2.4.2.18, 4.1.3.27 | 4.1.3.27 | KEGG PATHWAY mainly uses 2.4.2.18 |
4.1.3.31 | prpC | 2.3.3.1, 4.1.3.31 | 2.3.3.5 | 2.3.3.5 | 4.1.3.31 | inconsistency of EC (4.1.3.31 is changed to 2.3.3.1) |
4.1.3.9 | menD | 2.3.3.11, 4.1.1.71 | 2.5.1.64 | 2.5.1.64, 4.1.1.71 | 4.1.1.71 | inconsistency of EC (4.1.3.9 is changed to 2.3.3.11) |
4.2.1.13 | tdcG, yhaP-Q, sdhY | 4.2.1.13 | 4.3.1.17 | 4.3.1.17 | no EC | inconsistency of EC (4.2.1.13 is changed to 4.3.1.17) |
4.2.1.14 | sdaA-B | 4.3.1.17, 4.3.1.19 | 4.3.1.17 | 4.3.1.17 | no EC | possible misannotation by GEM System (4.2.1.14 is changed to 4 |
4.2.1.16 | tdcB, ilvA | 4.3.1.19 | 4.3.1.19 | 4.3.1.19 | no EC | inconsistency of EC (4.2.1.16 is changed to 4.3.1.19) |
4.2.99.11 | mgsA | 4.2.3.3 | 4.2.3.3 | 4.2.3.3 | 4.2.3.3 | inconsistency of EC (4.2.99.11 is changed to 4.2.3.3) |
4.2.99.2 | thrC | 4.2.99.2 | 4.2.3.1 | 4.2.3.1 | 4.2.3.1 | inconsistency of EC (4.2.99.2 is changed to 4.2.3.1) |
4.2.99.8 | cysK, M | 2.5.1.47 | 2.5.1.47 | 2.5.1.47 | 4.2.99.8 | inconsistency of EC (4.2.99.8 is changed to 2.5.1.47) |
4.2.99.9 | metB | 2.5.1.48 | 2.5.1.48 | 2.5.1.48 | 4.2.99.9 | inconsistency of EC (4.2.99.9 is changed to 2.5.1.48) |
4.3.1.8 | hemC | 2.5.1.61 | 2.5.1.61 | 2.5.1.61 | 4.3.1.8 | inconsistency of EC (4.3.1.8 is changed to 2.5.1.61) |
4.3.99.1 | cynS | 4.3.99.1 | 4.2.1.104 | 4.2.1.104 | no EC | inconsistency of EC (4.3.99.1 is changed to 4.2.1.104) |
4.6.1.3 | aroB | 4.6.1.3 | 4.2.3.4 | 4.2.3.4 | N.A. | inconsistency of EC (4.6.1.3 is changed to 4.2.3.4) |
4.6.1.4 | aroC | 4.6.1.4 | 4.2.3.5 | 4.2.3.5 | 4.2.3.5 | inconsistency of EC (4.6.1.4 is changed to 4.2.3.5) |
4.99.1.- | cysG | 4.99.1.4, 1.3.1.76, 2.1.1.107 | 4.99.1.4, 1.3.1.76, 2.1.1.107 | 4.99.1.4, 1.3.1.76, 2.1.1.107 | 2.1.1.107 | inconsistency of EC (incomplete EC) |
5.3.1.10 | nagB | 3.5.99.6 | 3.5.99.6 | left3.5.99.6 | 3.5.99.6 | inconsistency of EC (5.3.1.10 is changed to3.5.99.6) |
5.3.1.3 | fucI | 5.3.1.3, 5.3.1.25 | 5.3.1.3, 5.3.1.- | 5.3.1.25 | 5.3.1.25 | inconsistency of EC |
6.3.1.5 | yhjG | N.A. | N.A. | N.A. | N.A. | possible misannotation by GEM System by sequence similarity to nadE gene |
6.3.2.15 | murF | 6.3.2.15 | 6.3.2.10 | 6.3.2.10 | 6.3.2.15 | inconsistency of EC (6.3.2.15 is changed to 6.3.2.10) |
6.3.4.1 | guaA | 6.3.4.1, 6.3.5.2 | 6.3.4.1, 6.3.5.2 | 6.3.5.2 | 6.3.5.2 | KEGG PATHWAY mainly uses 6.3.5.2 |