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Table 2 Summary of individual pathway contrasts between three versions of model: The reference frames selected here is KEGG

From: Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

 

KEGG reference

In model

 

Reactions in pathway

Tfu_v1

Tfu_v2

Tfu_v3

Carbohydrates Metabolism

    

Glycolysis/Gluconeogenesis

45

28

62%

22

49%

15

33%

Citrate Cycle (TCA Cycle)

22

15

68%

15

68%

13

59%

Pentose Phosphate Pathway

40

20

50%

15

38%

13

33%

Pentose and Glucuronate Intrconv.

61

10

16%

8

13%

6

10%

Fructose and Mannose Metabolism

65

14

22%

14

22%

5

8%

Galactose Metabolism

38

12

32%

13

34%

8

21%

Starch and Sucrose Metabolism

74

14

19%

14

19%

12

16%

Amino Sugar and Nucleotide Metabolism

108

25

23%

21

19%

15

14%

Pyruvate Metabolism

64

26

41%

17

27%

15

23%

Glyoxylate and Dicarboxylate Metabolism

66

12

18%

11

17%

7

11%

Propanoate Metabolism

47

17

36%

14

30%

12

26%

Butanoate Metabolism

50

17

34%

12

24%

7

14%

C- 5 Branched Diabasic Acid Metabolism

18

3

17%

3

17%

1

6%

Inositol Phosphate Metabolism

43

4

9%

5

12%

4

9%

Amino Acid Metabolism

Ala, Asp and Glu Metabolism

43

21

49%

19

44%

18

42%

Gly, Ser and Thr Metabolism

63

11

17%

13

21%

9

14%

Cys and Met Metabolism

66

8

12%

3

5%

3

5%

Val, Leu and Ile Degradation

35

18

51%

13

37%

16

46%

Val, Leu and Ile Biosynthesis

14

10

71%

10

71%

7

50%

Lys Biosynthesis

30

13

43%

10

33%

8

27%

Lys Degradation

54

7

13%

8

15%

7

13%

Arg and Pro Metabolism

104

32

31%

26

25%

22

21%

His Metabolism

37

12

32%

13

35%

10

27%

Tyr Metabolism

66

11

17%

8

12%

9

14%

Phe Metabolism

70

11

16%

9

13%

9

13%

Trp Metabolism

69

14

20%

14

20%

9

13%

Phe, Tyr and Trp Biosynthesis

37

26

70%

16

43%

16

43%

  1. Each of these pathways were individually screened to make a call for active or inactive by tracing through the List of EC numbers on the KEGG map. If majority (almost all) of the EC number continuously connecting the pathway were present then the pathways was marked active else inactive.