These findings show that the respective degree of conservation of group A and group C MPK genes extends beyond primary sequence identity and is likely to be a feature of these genes in all eudicots.
Because InterProScan search algorithms include homology to aspects of proteins beyond primary sequence, including domain architecture, protein family, and predicted folding patterns, it is possible the some of the InterProScan homology results allow protein classification when BLAST does not.
To extend our analysis beyond primary sequence conservation for lncRNAs, we employed REAPR to identify lncRNA secondary structures and analyze their conservation across the anophelines.
It just means the community needs to move beyond primary sequence analysis.
For the folding of multidomain proteins, the subdomains act as the primary sequence and their intramolecular interactions drive supertertiary folding.
Extra complexity, even for single-subunit proteins, also comes with incorporation of additional structural features beyond the primary sequence, like disulphide linkages, metal ions, cofactors and post-translational modifications, and the use of non-standard amino acids (outwith the main 20).
Knowledge about conformational preferences and structural regularities, going beyond
Beyond their primary sequence, the two most striking conserved features of the AH domain are its high negative charge density and the distribution and orientation of its hydrophobic residues.
Note that the amino acid cysteine is absent in the primary sequence of both MBP and GB1.
Past a minimum primary distance of 6, however, the differences between the coevolving sites and all sites become constant suggesting that the tendency towards coevolution is indifferent to the degree of primary sequence separation beyond those separations strongly correlated to interactions within a secondary structure.
