Ancestral sequences reconstructed from individual species using an MSA limited to one sequence per species, with inserts unique to a single genus removed resulting in FastML joint (892 residues) and marginal (892 residues) sequences columns 6 and 7, Mega5 (770 residues) column 8, and PAML (679 residues) column 9.
Sequences derived from an MSA of the ancestors for the five major groups; amoebozoa, opisthokonts, kinetoplasts, alveolates, and stramenopiles FastML joint (856 residues) columns 2 and FastML marginal (856 residues) column 3 in figure 7 A, Mega5 (853 residues) column 4, PAML (819 residues) column 5. Rat is included in column 1 for comparison.
In marginal modes, residue emission probabilities involving missing data are the appropriate marginal summation of the state's emission probabilities.
FastML additionally has the option of marginal reconstruction (where the residue replaced is based on the posterior probability of the next step at that position from the tree), or joint reconstruction (where the probability is the product of the next two steps, that is, the next most likely substitution is based on two steps rather than one).
Further increase in temperature from 468 °C has contributed a marginal loss in weight leaving residue 14.6 % at 547 °C.
Residues 104 113 form a long loop with an alternation of hydrophilic and negative residues, and its marginal role in the GADD45 β–MKK7 protein protein interaction is probably due to the highly flexible nature of this portion of GADD45 β.
Next, we analyzed control untreated and H2O2-treated flies by OxICAT, and we found there was a marginal oxidation of the cysteine residues (26.3%; Figure 4B) in comparison to untreated control flies (22%; Figure 2B).
Consequently, the coenzyme specificity was not significantly changed, which suggests that this residue plays only a marginal role in coenzyme recognition.
Mutation to a negative residue such as Asp has marginal effects on the reduction potential, probably due to movement of the Asp side chain from His and its solvation.
The minimal essential region of GADD45 β that interacts with MKK7 is at residues 60 86, but another region (residues 104 113) seems to have a more marginal role to stabilize the interaction between GADD45 β and MKK7 (Papa et al).
