Towards a semi-automatic functional annotation tool based on decision tree techniques

MLSB'07

Subtilist functional hierarchy:

The number of proteins given for each class corresponds to the ones that are classified in this class or in his subclasses by annotator experts. Not all these proteins are taken into account to construct decision trees. We don't consider classes 4, 5 and 6 and we choose to consider only proteins that have at least an interpro identifier and at least a similar protein with a GO-term and a least a similar protein with a Swiss-Prot keyword.

Functional classnumber of proteins from L.sakei

number of proteins from L.bulgaricus

1 Cell envelope and cellular processes
367
449

1.1 Cell wall

25
86

1.2 Transport/binding proteins and lipoproteins

224
268

1.2.1 Transport/binding of proteins/peptides

8
39

1.2.2 Transport/binding of nucleic acids

0
0

1.2.3 Transport/binding of inorganic ions

57
32

1.2.4 Transport/binding of carbohydrates

30
18

1.2.5 Transport/binding of amino-acids

30
44

1.2.6 Transport/binding of nucleosides, nucleotides, purines and pyrimidines

12
2

1.3 Sensors (signal transduction)

26
24

1.4 Membrane bioenergetics (electron transport chain and ATP synthase)

8
28

1.5 Mobility and chemotaxis

0
0

1.6 Protein secretion

16
11

1.7 Cell division

23
17

1.8 Sporulation

0
0

1.9 Germination

0
0

1.10 Transformation/competence

8
19

2 Intermediary metabolism

349
315

2.1 Metabolism of carbohydrates and related molecules

106
106

2.1.1 Specific carbohydrate metabolic pathway

34
88

2.1.2 Main glycolytic pathways

19
17

2.1.3 TCA cycle

0
1

2.1.4 Substrate-specific entries to carbohydrate metabolic pathway

0
0

2.2 Metabolism of amino acids and related molecules

38
55

2.3 Metabolism of nucleotides and nucleic acids

82
75

2.4 Metabolism of lipids

54
38

2.5 Metabolism of coenzymes and prosthetic groups

40
34

2.6 Metabolism of phosphate

1
5

2.7 Metabolism of sulfur

0
0

2.8 Metabolism of nitrogen/nitrate and nitrite

0
2

2.9 Protein fate

23
0

3 Information pathways

377
381

3.1 DNA replication

34
19

3.2 DNA restriction and modification

12
14

3.3 DNA recombination and repair

47
43

3.4 DNA packaging and segregation

4
13

3.5 RNA synthesis

47
96

3.5.1 Transcription initiation

1
6

3.5.2 Transcription regulation

100
79

3.5.3 Transcription elongation

1
10

3.5.4 Transcription termination

2
1

3.6 RNA modification

34
29

3.7 Protein synthesis

107
97

3.7.1 Ribosomal proteins

57
56

3.7.2 Aminoacyl-tRNA synthetases

22
24

3.7.3 Translation initiation

6
3

3.7.4 Translation elongation

6
6

3.7.5 Translation termination

4
4

3.7.6 Nonribosomal protein synthesis

0
0

3.8 Protein modification

5
25

3.9 Protein folding

18
2

3.10 Protein degradation

0
43

4 Other functions

206
144

4.1 Adaptation to atypical conditions

40
16

4.2 Detoxification

20
7

4.3 Antibiotic production

0
0

4.4 Phage-related function

22
6

4.5 Transposon and IS

11
114

4.6 Miscellaneous

113
1

5 Proteins of unknown function that are similar to other proteins

345
462

5.1 Protein of unknown function similar to other proteins from the same organism

18
11

5.2 Protein of unknown function similar to proteins from other organisms

0
451

6 Protein of unknown function, without similarity to other proteins

229
280

Total

1873
2031
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