Table 3 Validation of E. coli model with KEGG and SWISS-PROT. Generated pathway model of E. coli was validated with E. coli specific entries of KEGG PATHWAY and SWISS-PROT database for every pathway. GEM System maintained high accuracy for proteins that are not EC coded. Three genes that are not identified actually correctly identified the gene, but in different organisms or strains. Similar table is available for all other models at the web database [29].
From: GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Pathway | EC coverage | Gene coverage | Genes without EC | Unidentified genes |
|---|---|---|---|---|
00010:Glycolysis/Gluconeogenesis | 26/26 (100%) | 43/44 (97%) | 1 | GPMA_ECOLI |
00051:Fructose and mannose | 26/26 (100%) | 53/53 (100%) | 3 | Â |
00052:Galactose metabolism | 17/17 (100%) | 28/28 (100%) | 2 | Â |
00061:Fatty acid biosynthesis (path 1) | 7/7 (100%) | 11/11 (100%) | 1 | Â |
00100:Biosynthesis of steroids | 10/10 (100%) | 9/10 (90%) | 0 | ISPH_ECOLI |
00130:Ubiquinone biosynthesis | 12/12 (100%) | 32/32 (100%) | 1 | Â |
00190:Oxidative phosphorylation | 8/8 (100%) | 41/41 (100%) | 1 | Â |
00511:N-Glycan degradation | 2/2 (100%) | 5/5 (100%) | 1 | Â |
00550:Peptidoglycan biosynthesis | 12/12 (100%) | 16/17 (94%) | 0 | UPK_ECOLI |
00620:Pyruvate metabolism | 33/33 (100%) | 45/45 (100%) | 1 | Â |
00640:Propanoate metabolism | 18/18 (100%) | 24/24 (100%) | 1 | Â |
00750:Vitamin B6 metabolism | 9/9 (100%) | 11/11 (100%) | 1 | Â |
00760:Nicotinate and nicotina | 16/16 (100%) | 16/16 (100%) | 1 | Â |
02010:ABC transporters prokaryotic | 4/4 (100%) | 190/190 (100%) | 186 | Â |
02020:Two-component system | 11/11 (100%) | 85/85 (100%) | 38 | Â |
02030:Bacterial chemotaxis | 3/3 (100%) | 20/20 (100%) | 17 | Â |
02040:Flagellar assembly | 1/1 (100%) | 38/38 (100%) | 37 | Â |
02060:Phosphotransferase sys | 2/2 (100%) | 53/53 (100%) | 13 | Â |
03010:Ribosome | 0/0 (%) | 55/55 (100%) | 55 | Â |
03030:DNA polymerase | 1/1 (100%) | 13/13 (100%) | 1 | Â |
03060:Protein export | 2/2 (100%) | 17/17 (100%) | 15 | Â |
03070:Type III secretion system | 1/1 (100%) | 10/10 (100%) | 9 | Â |
03090:Type II secretion system | 2/2 (100%) | 25/25 (100%) | 23 | Â |