TABLE 2.

Functional categories of 560 genes whose expression is significantly affected by the scoC4 mutation

Classification	No. of genes
	Total	Affected
1. Cell envelope and cellular processes
1.1. Cell wall	108	12
1.2. Transport/binding proteins and lipoproteins	388	76
1.3. Sensors (signal transduction)	38	1
1.4. Membrane bioenergetics (electron transport and ATP synthesis)	74	6
1.5. Mobility and chemotaxis	55	29
1.6. Protein secretion	20	2
1.7. Cell division	21
1.8. Sporulation	152	37
1.9. Germination	20	1
1.10. Transformation and competence	21
2. Intermediary metabolism
2.1. Metabolism of carbohydrates and related molecules
2.1.1. Specific pathways	215	38
2.1.2. Main glycolytic pathways	27	3
2.1.3. Tricarboxylic acid cycle	18	3
2.2. Metabolism of amino acids and related molecules	199	47
2.3. Metabolism of nucleotides and nucleic acids	83	27
2.4. Metabolism of lipids	82	9
2.5. Metabolism of coenzymes and prosthetic groups	104	1
2.6. Metabolism of phosphate	10	2
2.7. Metabolism of sulfur	9
3. Information pathways
3.1. DNA replication	24	3
3.2. DNA restriction/modification and repair	39	1
3.3. DNA recombination	19
3.4. DNA packaging and segregation	9
3.5. RNA synthesis
3.5.1. Initiation	20	2
3.5.2. Regulation	212	11
3.5.3. Elongation	7	1
3.5.4. Termination	4
3.6. RNA modification	21
3.7. Protein synthesis
3.7.1. Ribosomal proteins	55	35
3.7.2. Aminoacyl-tRNA synthetases	28	1
3.7.3. Initiation	6	1
3.7.4. Elongation	6	1
3.7.5. Termination	3	1
3.8. Protein modification	27	5
3.9. Protein folding	8
4. Other functions.
4.1. Adaptation to atypical conditions	71	15
4.2. Detoxification	70	4
4.3. Antibiotic production	28	3
4.4. Phage-related functions	87	3
4.5. Transposon and IS	10	2
4.6. Miscellaneous	25
5. Similar to unknown proteins
5.1. From B. subtilis	178	24
5.2. From other organisms	477	36
6. No similarity	1,049	106