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Table 2 Functional categories (FunCat level 2) and their abundance in archaeal and bacterial effectomes

From: Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions

FunCat Category

Description

Archaea

Bacteria

  

HT

MS

AQU

ANE

AB

TH

MS

PS

AQU

TER

HOA

AER

ANE

NHAL

MHAL

HITR

2.01

Glycolysis and gluconeogenesis

+

-0.32

-0.01

-0.17

0.49

0.34

0.52

0.42

0.44

0.51

0.46

0.35

0.55

0.56

0.36

0.60

2.04

Glyoxylate cycle

x

x

x

x

0.20

+

0.20

+

0.20

0.45

-0.12

0.30

+

0.34

+

-0.78

2.07

Pentose-phosphate pathway

-

-

-

-

0.00

-0.32

0.00

0.03

-0.03

0.12

-0.12

-0.26

0.09

0.04

 

0.23

2.08

Pyruvate dehydrogenase complex

x

x

x

x

0.35

-

0.40

+

+

+

0.40

0.08

x

0.60

+

0.73

2.09

Anaplerotic reactions

x

x

x

x

0.48

+

0.48

+

+

+

+

0.60

+

+

+

0.00

2.10

Tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle)

x

+

+

x

0.49

+

0.50

0.40

0.51

0.58

0.37

0.58

0.43

0.49

0.46

0.39

2.11

Electron transport and membrane-associated energy conservation

0.10

0.30

0.10

0.25

0.28

0.18

0.28

0.21

0.32

0.37

0.22

0.31

0.21

0.26

0.28

0.25

2.30

Photosynthesis

x

x

x

x

-0.12

-

-0.12

x

-0.12

0.33

-0.48

-0.60

+

-0.48

x

-0.30

2.45

Energy conversion and regeneration

+

0.29

+

+

0.32

0.19

0.31

0.30

0.39

0.44

0.23

0.39

0.17

0.29

0.27

0.33

12.01

Ribosome biogenesis

0.79

0.85

0.79

0.82

1.03

0.92

1.04

1.00

1.07

1.06

0.94

1.05

1.00

1.07

1.08

1.10

12.04

Translation

0.63

0.66

0.62

0.65

0.84

0.73

0.85

0.82

0.88

0.87

0.75

0.86

0.81

0.87

0.90

0.91

12.07

Translational control

+

+

+

+

0.68

+

0.68

+

0.64

+

0.65

0.75

+

0.74

+

0.75

12.10

Aminoacyl-tRNA synthetases

-

-

-

-

-0.32

-

-0.32

-

-

-

-

-

-

-

-

0.21

14.01

Protein folding and stabilization

+

0.46

+

+

0.45

0.53

0.47

0.35

0.46

0.55

0.36

0.48

0.46

0.46

0.50

0.52

32.07

Detoxification

+

-

+

+

0.09

0.20

0.09

0.10

0.11

0.20

-0.01

0.09

0.00

0.12

0.15

0.26

34.01

Homeostasis

+

-

+

+

0.09

-0.02

0.11

0.02

0.13

0.12

0.03

0.07

0.10

0.07

0.02

0.22

34.05

Cell motility

-

+

0.08

0.01

-0.04

-0.08

-0.02

-0.22

-0.25

0.16

0.17

0.12

0.06

-0.09

-0.38

-0.50

42.33

Pilus/fimbria

x

x

x

x

0.00

0

0.00

+

+

0

-0.40

0.18

-

0.00

+

0.00

70.03

Cytoplasm

x

x

x

x

0.02

-0.07

0.03

0.03

0.04

0.08

-0.02

0.05

-0.01

0.04

0.05

0.10

70.27

Extracellular/secretion proteins

+

-

+

+

0.34

+

0.36

+

0.18

0.22

0.39

0.28

0.40

0.44

+

0.26

70.34

Prokaryotic cell envelope component

x

x

x

x

0.05

x

0.07

0.02

0.01

0.04

0.09

-0.04

-0.14

0.17

0.07

0.12

  1. For archaeal and bacterial genomes, the number of gene products contributing to FunCat categories of level 2 was determined (see Methods). The columns lists the ratio log(fEff(Cat)/fAll(Cat)) for the categories, if #All(Cat) was at least 100 (compare Table 1). In all other cases a trend is given indicated by a "+" for overrepresentation, a "-" for underrepresentation and a 0 for a score value of 0.0. An "x" indicates categories not occurring in the respective dataset. Abbreviations of subsets: AB all Bacteria, HT hyperthermophilic, TH thermophilic, MS mesophilic, PS psychrophilic, AQU aquatic, TER terrestrial, HOA host-associated, AER aerobic, ANE anaerobic, NHAL non halophilic, MHAL moderately halophilic species, and HITR the subset of bacterial species possessing an extreme number of tRNA genes, i.e. MG_CUB(Bacteria_HITR).
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BMC Genomics

ISSN: 1471-2164

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