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The main parts of this nuclear gene tree [14] have nevertheless been supported in later studies based on far more comprehensive alignments [e.g. 17] and genome level characters like retroposon insertion and indel differences [18] [20].
In Additional file 1: Figures S2 to S6, we provide more comprehensive alignments, which include one representative of each genus and display their predicted secondary structure.
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The more comprehensive alignment found in File S1 was used to calculate the scores but Figure 4 can illustrate the conservation pattern of the predicted SDPs within their sequence context and also the identity of the residues for each PAT.
A more comprehensive alignment is presented in the Supplementary Information and Guillemin et al. To obtain soluble stable recombinant human Bcl-B (Uniprot: Q9HD36) protein from E. coli fermentations for our structural studies, we mutated the cysteines 20 and 128 to serine and deleted 27 C-terminal residues in the predicted TM region.
(A more comprehensive alignment, including several typical plant SKP1-like proteins, is shown in [ Additional Figure 2].) Only two amino acids, not among the key residues predicted to be involved in binding an F-box domain (Huang et al. 2006), are different between PiSSK1 and PhSSK1, suggesting that an SSK1 orthologue is present in P. inflata.
Currently, the final Galinter alignments of NCIVs are ranked by their size in terms of the number of involved NCIVs, but a more comprehensive scoring function for alignments is desirable.
However, a more thorough sequence conservation analysis, involving comprehensive alignments and conservation measurements, has the potential to be much more powerful.
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Firstly, it augmented the Archimate modelling notation with the constructs of the Business Motivation Model (BMM) to present a more comprehensive technique of modelling strategic alignment of business and IT.
Other studies [14], [19], [40] have favored the same topology using shorter alignments but a more comprehensive taxon sampling.
Another advantage of DOMAIN is that often it provides a more comprehensive means of interpreting the identified network alignments, because protein domains are directly relevant to function in many cases.
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