Table 2

Examples of functional categories of core genome components in five Streptomyces genomes.

Function description

Examples of GO classes

No. families


Genetic information processing

GO:0006260 (DNA replication)

27

GO:0006350 (transcription)

174

GO:0006412 (translation)

102

GO:0006310 (DNA recombination)

14

GO:0004803 (transposase activity)

4

GO:0015074 (DNA integration)

2


Regulation

GO:0003700 (sequence-specific DNA binding transcription factor activity)

201

GO:0016566 (specific transcriptional repressor activity)

43

GO:0000155 (two-component sensor activity)

36

GO:0000156 (two-component response regulator activity)

49

GO:0016987 (sigma factor activity)

31


Metabolism

GO:0005975 (carbohydrate metabolic process)

67

GO:0009058 (biosynthetic process)

66

GO:0009116 (nucleoside metabolic process)

13

GO:0006520 (cellular amino acid metabolic process)

12

GO:0006631 (fatty acid metabolic process)

7


Morphogenesis

GO:0007047 (cellular cell wall organization)

14

GO:0007059 (chromosome segregation)

9

GO:0000902 (cell morphogenesis)

3

GO:0000917 (barrier septum formation)

2


Response to stimulus

GO:0006950 (response to stress)

22

GO:0046677 (response to antibiotic)

12

GO:0009432 (SOS response)

9

GO:0006979 (response to oxidative stress)

3


Transport

GO:0006811 (ion transport)

14

GO:0015904 (tetracycline transport)

9

GO:0015031 (protein transport)

8

GO:0006817 (phosphate transport)

6

GO:0006865 (amino acid transport)

6

GO:0008643 (carbohydrate transport)

6


Hydrolase

GO:0008233 (peptidase activity)

38

GO:0016810 (hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds)

22

GO:0004553 (hydrolase activity, hydrolyzing O-glycosyl compounds)

19

GO:0016788 (hydrolase activity, acting on ester bonds)

12

GO:0016820 (hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances)

10

GO:0016799 (hydrolase activity, hydrolyzing N-glycosyl compounds)

7

GO:0030245 (cellulose catabolic process)

3

GO:0004568 (chitinase activity)

2


Ion binding

GO:0008270 (zinc ion binding)

52

GO:0051536 (iron-sulfur cluster binding)

45

GO:0000287 (magnesium ion binding)

29

GO:0005506 (iron ion binding)

26


Zhou et al. BMC Bioinformatics 2012 13(Suppl 10):S8   doi:10.1186/1471-2105-13-S10-S8

Open Data