Table 1

Examples of potentially "new" and "old" interacting pairs of proteins whose co-evolution was evaluated using two sets of organisms

Protein

Level9(= all)

Nearest2


Tot/+

AUC

Interactor (corr)

Tot/+

AUC

Interactor (corr)


MINE_ECOLI

Cell division topological specificity factor

846/1

0.12

MIND_ECOLI (0.52)

223/1

0.83

MIND_ECOLI (0.60)


"recent"

(BINARY_PHYS)

PABA_ECOLI

Para-aminobenzoate synthase glutamine amidotransferase component II

671/1

0.28

PABB_ECOLI (0.49)

106/1

0.96

PABB_ECOLI (0.96)


DHAS_ECOLI

Aspartate-semialdehyde dehydrogenase

760/1

0.17

DNAK_ECOLI (0.48)

384/1

0.81

DNAK_ECOLI (0.90)


GSHB_ECOLI

Glutathione synthetase

755/1

0.30

AMPM_ECOLI (0.61)

375/1

0.93

AMPM_ECOLI (0.95)


DPO3A_ECOLI

DNA polymerase III subunit alpha

306/1

0.70

DPO3E_ECOLI (0.73)

128/1

0.11

DPO3E_ECOLI (0.57)


DPO3E_ECOLI

DNA polymerase III subunit epsilon

357/1

0.64

DPO3A_ECOLI (0.73)

123/1

0.22

(0.57) max


RPOB_ECOLI

DNA-directed RNA polymerase subunit beta

280/7

0.82

(0.98) max

126/4

0.48

(0.93) max


"old"

(COMPLEXES)

RPOA_ECOLI

DNA-directed RNA polymerase subunit alpha

258/6

0.81

(0.80) max

90/3

0.48

(0.93) max


ZNUB_ECOLI

High-affinity zinc uptake system membrane protein znuB

370/2

1.00

(0.87) max

129/1

0.36

ZNUC_ECOLI (0.74)


ZNUC_ECOLI

Zinc import ATP-binding protein ZnuC

386/2

0.99

(0.87) max

123/2

0.41

(0.74) max


ZNUA_ECOLI

High-affinity zinc uptake system protein znuA

395/2

0.98

(0.87) max

39/1

0.79

ZNUC_ECOLI (0.74)


The co-evolution between these proteins was evaluated using the "level9" and "nearest2" sets of organisms. The total number of pairs involving each protein for which it was possible to make calculations, as well as the number of positives (+) are indicated. The co-evolutionary score with the interactor is also shown (corr). For the cases for which the list contain more than one positive the score is the highest one (max). Finally, the AUC value for the list of scores is also included.

Herman et al. BMC Bioinformatics 2011 12:363   doi:10.1186/1471-2105-12-363

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