The C19 residue of the BR alignment is strikingly conserved in all vertebrates and invertebrates in the ATF2, ATF3, NFE2, BACH, CREB, FOS, JUN, L-MAF, S-MAF families (for a complete alignment of the BR domains of all bZIP proteins, see Additional file 1).
A complete alignment indicates low divergence, whereas an incomplete alignment indicates substantial divergence.
We computed ω = Ka/ Ks for the complete alignment, ω A = Ka A/ Ks A for the adjacent alignment, and ω 1 = Ka I/ Ks I for the isolated alignment.
A multiple alignment of 1000 distinct S-helix representatives detected in our searches from across the three superkingdoms of Life were used to construct a comprehensive multiple alignment (Fig. 2; see additional file 1 for complete alignment) and a sequence logo quantifying the conservation at each position was derived from this alignment (Fig 3) [ 39].
The parameters used for the simulation were obtained by optimizing a GTR + I + Γ4 model for the complete alignment and ML tree with RAxML [ 92].
The trend for the distribution of scores for complete alignment (SCA) was similar to SAP scores; 59% aSVRs scored higher and 14% scored lower than bSVRs (see Text S1 and Figure S1).
Alignment of these sequences with AtRaptor1A, AtRaptor1B, mammalian Raptor, the budding yeast Raptor homologue KOG1 and the fission yeast Raptor homologue Mip1p showed that there is a striking degree of conservation among all Raptor homologues (Fig. 1A; for the complete alignment [see additional file 1]).
For the complete alignment we tested for appropriate models of nucleotide substitution using the Akaike Information Criterion (AIC) as implemented in Modeltest [ 42].
We used the method of Yang and Nielsen [ 15], as implemented in PAML (yn00, version 3.15), to estimate Ka and Ks for each complete alignment (no partitioning) and its two subalignments.
This expanded alignment confirmed the structure prediction for this motif and suggested that it consisted of a single long α-helix, which would form a CC (See additional file 1 for complete alignment).
The due date for my draft was January 15th, and I came back to WWE full time on the road at the beginning of January, so it became a fiasco!" There is often conflict between the subjects of autobiographies and their ghost writer, and with such a complicated industry as professional wrestling a key component of the book, the need for complete alignment was essential.
