Table 2

Representative proteins used to compute Figure 2. Class is the COG functional code [18]. Rank is rank in a list of most conserved proteins (families of orthologs), from 0 to 199, for the set of genomes under study; thus FtsH (rank 2) is more conserved than DNA polymerase I (rank 59). Coeff, S. Dev, and Max are respectively the correlation coefficient, the standard deviation, and the maximum elementwise difference between the scaled distance matrix given by this protein and the consensus distance matrix. Distances for this set of organisms were approximately 0–150. Each sequence was limited to the most conserved 300-long amino acid sequence for the protein.

Gene

Class

Name

COG

Rank

Coeff

S.Dev

Max


GidA

D

glucose-inhibited division protein

0445

23

.92

4.27

11.90

-

R

GTP-binding protein

0012

43

.94

3.84

12.43

RuvB

L

Holliday junction DNA helicase

2255

19

.89

4.32

12.51

Pnp

J

polynucleotide phosphorylase

1185

25

.86

4.94

13.11

PyrG

F

CTP synthetase

0504

26

.91

4.19

13.95

LepA

N

GTP-binding elongation factor

0481

15

.92

4.88

14.00

DnaX

L

DNA polymerase III subunits gamma and tau

2812

86

.90

4.37

14.59

Mfd

LK

transcription-repair coupling factor

1197

31

.88

4.82

14.94

UvrB

L

DNA excision nuclease subunit B

0556

12

.93

4.44

16.29

InfB

J

translation initiation factor IF-2

0532

32

.90

4.59

17.46

Exo

L

DNA polymerase I

0258

59

.89

4.85

17.60

PolC

L

DNA polymerase III, alpha chain

0587

61

.77

6.43

17.81

RecA

L

RecA protein

0468

4

.85

6.22

19.18

GyrA

L

DNA gyrase subunit A

0188

10

.88

5.60

19.74

HflB

0

cell division protein FtsH

0465

2

.86

5.29

19.89

ClpX

O

ATP-dependent Clp protease, ClpX

1219

13

.89

5.12

20.10

ThrS

J

threonyl-tRNA synthetase

0441

33

.77

6.94

20.19

Rho

K

transcription termination factor rho

1158

3

.87

5.83

20.20

GroL

O

GroEL, chaperone Hsp60

0459

8

.92

5.90

20.35

ClpB

0

ClpB protein

0542

7

.75

6.23

21.01

-

R

putative GTP-binding protein

1160

165

.94

7.93

21.07

DnaK

0

dnaK, chaperone Hsp70

0443

5

.81

6.48

21.27

RpSA

J

30S ribosomal subunit protein S1

0539

38

.88

8.14

22.48

RpoA

K

DNA-directed RNA polymerase alpha chain

0202

102

.91

10.93

32.41

TrxB

0

thioredoxin reductase

0492

66

.87

8.67

32.54

UvrC

L

excinuclease ABC subunit C

0322

133

.93

6.67

32.68

NusA

K

transcription pausing

0195

106

.83

11.11

39.39

QRI7

O

o-sialoglycoprotein endopeptidase

0533

123

.89

7.53

43.68

YidC

N

60 kD inner membrane protein

0706

179

.85

13.69

53.24

SecY

N

subunit of translocase

0201

82

.86

8.00

58.78


Bern and Goldberg BMC Evolutionary Biology 2005 5:34   doi:10.1186/1471-2148-5-34

Open Data