Table 1 |
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Examples of potentially "new" and "old" interacting pairs of proteins whose co-evolution was evaluated using two sets of organisms |
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Protein |
Level9(= all) |
Nearest2 |
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|
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|
Tot/+ |
AUC |
Interactor (corr) |
Tot/+ |
AUC |
Interactor (corr) |
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|
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MINE_ECOLI |
Cell division topological specificity factor |
846/1 |
0.12 |
MIND_ECOLI (0.52) |
223/1 |
0.83 |
MIND_ECOLI (0.60) |
|
|
|
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|
"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) |
|
|
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|
DHAS_ECOLI |
Aspartate-semialdehyde dehydrogenase |
760/1 |
0.17 |
DNAK_ECOLI (0.48) |
384/1 |
0.81 |
DNAK_ECOLI (0.90) |
|
|
|
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|
GSHB_ECOLI |
Glutathione synthetase |
755/1 |
0.30 |
AMPM_ECOLI (0.61) |
375/1 |
0.93 |
AMPM_ECOLI (0.95) |
|
|
|
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|
DPO3A_ECOLI |
DNA polymerase III subunit alpha |
306/1 |
0.70 |
DPO3E_ECOLI (0.73) |
128/1 |
0.11 |
DPO3E_ECOLI (0.57) |
|
|
|
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DPO3E_ECOLI |
DNA polymerase III subunit epsilon |
357/1 |
0.64 |
DPO3A_ECOLI (0.73) |
123/1 |
0.22 |
(0.57) max |
|
|
|
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|
RPOB_ECOLI |
DNA-directed RNA polymerase subunit beta |
280/7 |
0.82 |
(0.98) max |
126/4 |
0.48 |
(0.93) max |
|
|
|
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|
"old" (COMPLEXES) |
RPOA_ECOLI |
DNA-directed RNA polymerase subunit alpha |
258/6 |
0.81 |
(0.80) max |
90/3 |
0.48 |
(0.93) max |
|
|
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|
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) |
|
|
|
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ZNUC_ECOLI |
Zinc import ATP-binding protein ZnuC |
386/2 |
0.99 |
(0.87) max |
123/2 |
0.41 |
(0.74) max |
|
|
|
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|
ZNUA_ECOLI |
High-affinity zinc uptake system protein znuA |
395/2 |
0.98 |
(0.87) max |
39/1 |
0.79 |
ZNUC_ECOLI (0.74) |
|
|
|
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|
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. |
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|
Herman et al. BMC Bioinformatics 2011 12:363 doi:10.1186/1471-2105-12-363 |
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