Table 2.
Summary of the numbers of proteins, reactions, and connected reactions in KEGG metabolic pathways predicted from the genome sequence and MS/MS identified proteins (Pathways with many predicted proteins but low connectivity are shaded).
| Metabolism | Metabolic pathway/ cellular process |
Genomics Prediction | All proteomic data | OD 0.7 | OD 1.2 | OD 0.7 versus OD 1.2 b | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| # predicted proteins |
# Reactions | # Connected reactions a |
#MS identified proteins (# single hit proteins) |
% identified proteins |
# Connected reactions with identified proteins a |
#MS identified proteins (# single hit proteins) |
% identified proteins |
# Connected reactions with identified proteins a |
#MS identified proteins (# single hit proteins) |
% identified proteins |
# Connected reactions with identified proteins a |
# proteins in OD 0.7 only | # proteins with ≥ 3X Peptides identified in OD 0.7 |
# proteins with ≥ 3X Peptides identified in OD 1.2 |
# proteins in OD 1.2 only | ||
| Carbohydrates | Glycolysis/ Gluconeogenesis * |
65 | 27 | 27 | 44(6) | 67.7 | 23 | 42(5) | 64.6 | 21 | 44(6) | 67.7 | 23 | 0 | 2 | 0 | 1 |
| Citrate cycle (TCA cycle) * |
29 | 17 | 16,1 | 24(1) | 82.8 | 15,1 | 24(1) | 82.8 | 15,1 | 23(1) | 79.3 | 15,1 | 1 | 1 | 0 | 0 | |
| Pentose phosphate pathway * |
24 | 17 | 8,9 | 20(4) | 83.3 | 8,6,2 | 20(4) | 83.3 | 8,6,2 | 18(3) | 75.0 | 7,6,1 | 1 | 0 | 1 | 0 | |
| Fructose and mannose metabolism * |
22 | 14 | 8,4,1,1 | 13(2) | 59.1 | 6,4 | 13(2) | 59.1 | 6,4 | 12(1) | 54.5 | 5,4 | 0 | 0 | 0 | 0 | |
| Starch and sucrose metabolism * |
19 | 18 | 4,3,3, 3,2,1, 1,1 |
12(4) | 63.2 | 3,3,3, 1,1 |
10(3) | 52.6 | 2,2,1, 1,1 |
12(4) | 63.2 | 3,3,3, 1,1 |
0 | 0 | 1 | 1 | |
| Amino sugar and nucleotide sugar metabolism * |
18 | 15 | 7,4,2,2 | 13(3) | 72.2 | 6,2,2,2 | 9(0) | 50.0 | 2,2,2, 2,1 |
13(3) | 72.2 | 2,4,2, 2,2 |
0 | 0 | 0 | 0 | |
| Pyruvate metabolism * |
44 | 19 | 19 | 34(1) | 77.3 | 18 | 34(1) | 77.3 | 17 | 34(1) | 77.3 | 17 | 0 | 3 | 1 | 0 | |
| Glyoxylate and dicarboxylate metabolism |
15 | 11 | 9,1,1 | 10(0) | 66.7 | 9,1 | 8(0) | 53.3 | 4,4,1 | 10(0) | 66.7 | 6.4 | 0 | 0 | 2 | 2 | |
| Propanoate metabolism |
38 | 11 | 7,2,1,1 | 32(0) | 84.2 | 7,2,1,1 | 31(0) | 81.6 | 5,2,1,1 | 32(0) | 84.2 | 5,2,1,1 | 0 | 2 | 1 | 1 | |
| Butanoate metabolism | 46 | 14 | 4,3,2, 1,1,1, 1,1 |
36(1) | 78.3 | 4,3,2, 1,1 |
36(1) | 78.3 | 4,3,2, 1,1 |
34(1) | 73.9 | 4,3,2,1 | 2 | 4 | 2 | 0 | |
|
| |||||||||||||||||
| Energy | Nitrogen metabolism * |
30 | 15 | 12,2,1 | 14(1) | 46.7 | 9,1 | 13(1) | 43.3 | 9,1 | 13(0) | 43.3 | 8,1 | 0 | 0 | 5 | 1 |
|
| |||||||||||||||||
| Lipids | Fatty acid metabolism * | 48 | 27 | 4,4,3,3(×5),1 | 36(1) | 75.0 | 4,4,3,3(×5),1 | 35(1) | 72.9 | 4,4,3,3(×5),1 | 36(1) | 75.0 | 4,4,3, 3(5),1 |
0 | 2 | 3 | 1 |
| Glycerolipid metabolism |
12 | 4 | 4 | 7(1) | 58.3 | 2,1 | 6(0) | 50.0 | 1,1 | 7(1) | 58.3 | 2,1 | 0 | 0 | 1 | 0 | |
|
| |||||||||||||||||
| Nucleotides | Purine metabolism * | 64 | 54 | 49,1,1, 1,1,1,1 |
43(2) | 67.2 | 32,5,1, 1,1 |
42(1) | 65.6 | 32,5,1, 1,1 |
39(1) | 60.9 | 30,5,1, 1,1,1 |
3 | 4 | 1 | 0 |
| Pyrimidine metabolism * |
51 | 45 | 40,1,1, 1,1,1 |
38(4) | 74.5 | 39,1,1 | 37(2) | 72.5 | 39 | 38(4) | 74.5 | 39,1,1 | 1 | 3 | 2 | 0 | |
|
| |||||||||||||||||
| Amino Acids | Alanine, aspartate and glutamate metabolism * | 25 | 17 | 17 | 19(2) | 76.0 | 13 | 19(2) | 76.0 | 13 | 17(0) | 68.0 | 11 | 0 | 3 | 1 | 0 |
| Glycine, serine and threonine metabolism * |
35 | 17 | 6,9,1,1 | 24(1) | 68.6 | 9,6,1 | 23(1) | 65.7 | 9,6,1 | 23(0) | 65.7 | 8,6,1 | 0 | 2 | 4 | 1 | |
| Cysteine and methionine metabolism * |
19 | 19 | 12,4,1, 1,1 |
13(2) | 68.4 | 8,3,4, 1,1 |
13(2) | 68.4 | 8,3,4, 1,1 |
11(0) | 57.9 | 6,3,2, 1,1,1 |
0 | 1 | 1 | 0 | |
| Valine, leucine and isoleucine degradation * |
40 | 24 | 4(×3),2(×3), 2,2,2 |
34(0) | 85.0 | 4(×3),4,2(×3),2 | 33(0) | 82.5 | 4(×3),4,2(×3),2 | 34(0) | 85.0 | 4(3),4,2(3),2 | 0 | 1 | 3 | 1 | |
| Valine, leucine and isoleucine biosynthesis * |
25 | 24 | 24 | 22(2) | 88.0 | 24 | 22(2) | 88.0 | 24 | 20(1) | 80.0 | 23 | 1 | 1 | 2 | 0 | |
| Lysine biosynthesis * |
16 | 15 | 8,4,3 | 13(2) | 81.3 | 7,4,3 | 12(1) | 75.0 | 7,3,3 | 13(2) | 81.3 | 7,4,3 | 0 | 2 | 0 | 0 | |
| Lysine degradation | 27 | 6 | 2,2,1,1 | 23(0) | 85.2 | 2,2,1,1 | 23(0) | 85.2 | 2,2,1,1 | 23(0) | 85.2 | 2,2,1,1 | 0 | 1 | 1 | 0 | |
| Arginine and proline metabolism * |
44 | 24 | 15,3,2, 1,1,1,1 |
28(4) | 63.6 | 7,3,3, 2,1,1, 1,1 |
26(3) | 59.1 | 6,3,3, 2,1,1, 1,1 |
26(2) | 59.1 | 4,3,3, 3,1,1, 1,1 |
0 | 2 | 1 | 1 | |
| Histidine metabolism * |
25 | 15 | 7,7,1 | 15(0) | 60.0 | 6,2,2, 1,1 |
14(0) | 56.0 | 6,2,1, 1,1 |
15(0) | 60.0 | 6,2,2, 1,1 |
0 | 1 | 1 | 1 | |
| Tyrosine metabolism |
24 | 6 | 2,1,1, 1,1 |
12(1) | 50.0 | 1,1,1 | 11(1) | 45.8 | 1,1,1 | 12(1) | 50.0 | 1,1,1 | 0 | 2 | 1 | 1 | |
| Tryptophan metabolism |
33 | 10 | 2,2,2, 1,1,1,1 |
27(0) | 81.8 | 2,2,1, 1,1,1,1 |
27(0) | 81.8 | 2,2,1, 1,1,1,1 |
27(0) | 81.8 | 2,2,1, 1,1,1,1 |
0 | 1 | 3 | 0 | |
| Phenylalanine, tyrosine and tryptophan biosynthesis * |
26 | 19 | 19 | 15(2) | 57.7 | 12,2,1 | 15(2) | 57.7 | 12,2,1 | 15(2) | 57.7 | 12,2,1 | 0 | 3 | 1 | 0 | |
|
| |||||||||||||||||
| Other Amino Acids | Beta-Alanine metabolism * | 22 | 7 | 3,2,1,1 | 16(1) | 72.7 | 3,2 | 15(0) | 68.2 | 2,2 | 16(1) | 72.7 | 3,2 | 0 | 0 | 1 | 0 |
| Selenoamino acid metabolism * |
10 | 8 | 4,4 | 6(0) | 60.0 | 3,3 | 6(0) | 60.0 | 3,3 | 6(0) | 60.0 | 3,3 | 0 | 0 | 0 | 0 | |
|
| |||||||||||||||||
| Cofactors and Vitamins | Ubiquinone and other terpenoid-quinone biosynthesis | 8 | 10 | 4,2,2, 1,1 |
3(1) | 37.5 | 4,1,1 | 3(1) | 37.5 | 4,1,1 | 3(1) | 37.5 | 4,1,1 | 0 | 0 | 0 | 0 |
| One carbon pool by folate * |
17 | 15 | 15 | 13(1) | 76.5 | 12 | 10(1) | 58.8 | 11 | 12(0) | 70.6 | 11 | 0 | 0 | 4 | 3 | |
| Thiamine metabolism * |
9 | 8 | 6,2 | 5(0) | 55.6 | 4,1 | 3(0) | 33.3 | 3,1 | 5(0) | 55.6 | 4,1 | 0 | 1 | 1 | 2 | |
| Riboflavin metabolism * |
5 | 5 | 4,1 | 3(1) | 60.0 | 2,1 | 3(1) | 60.0 | 2,1 | 3(1) | 60.0 | 2,1 | 0 | 0 | 1 | 0 | |
| Pantothenate and CoA biosynthesis |
15 | 11 | 6,3,1,1 | 12(3) | 80.0 | 5,3,1 | 10(1) | 66.7 | 5,1 | 10(2) | 66.7 | 5,3,1 | 1 | 0 | 0 | 0 | |
| Folate biosynthesis |
9 | 12 | 5,3,2, 1,1 |
3(1) | 33.3 | 2,1,1 | 2(0) | 22.2 | 1,1 | 3(1) | 33.3 | 1,1,1 | 0 | 0 | 1 | 0 | |
| Nicotinate and nicotinamide metabolism * |
12 | 11 | 11 | 5(1) | 41.7 | 7 | 4(0) | 33.3 | 2,2,1 | 5(1) | 41.7 | 7 | 0 | 1 | 0 | 0 | |
| Porphyrin and chlorophyll metabolism * |
25 | 32 | 15,7,6, 2,1,1 |
20(4) | 80.0 | 8,7,4, 4,2,1 |
18(2) | 72.0 | 8,7,3, 2,1,1, 1,1 |
17(3) | 68.0 | 7,4,3, 1,1,1,1 |
2 | 0 | 0 | 0 | |
|
| |||||||||||||||||
| Biosynthesis of Polyketides and Terpenoids | Terpenoid backbone biosynthesis * | 14 | 11 | 4,3,3,1 | 11(0) | 78.6 | 4,2,1 | 11(0) | 78.6 | 4,2,1 | 11(0) | 78.6 | 4,2,1 | 0 | 1 | 1 | 0 |
| Carotenoid biosynthesis |
2 | 5 | 5 | 2(0) | 100.0 | 5 | 2(0) | 100.0 | 5 | 2(0) | 100.0 | 5 | 0 | 0 | 0 | 0 | |
a
Number of reactions within each “cluster of linked reaction(s)” separated by commas. Number in parenthesis indicates the number reaction cluster catabolized by the same enzyme(s).
b
The numbers included only the proteins with at least 2 unique peptide identifications.
*
Indicate the biomodules seemed to contain sufficient number of connected reactions (predicted proteins) to drive the functions.