Global sequence alignment, similarity

Figure 2 shows a global alignment of selected thionin sequences. The background color for a given residue indicates the degree of conservation of that residue in a particular position in the sequence. It is clear that thionins are highly conserved over different species. Based on their conserved sequences and similar three-dimensional structures it is reasonable to assume a common mode of action for all thionins. 

There are two approaches of sequence alignments A global alignment compares similarity across the full stretch of sequences, while a local alignment searches for regions of similarity in parts of the sequences. 

The global superposition of enzymes of family 13 on the common (/ /a)8 barrel is remarkably efficient to start /Joe loops comparison in the 3D space. This 3D superposition can focus directly to the new structural information for similar enzymes in term of functionality when compared to predictions based on sequence alignment. Interestingly, it has been seen in some comparisons, between less similar enzymes, that our 3D superposition is more powerful and more accurate to match segments of residues whose location is tightly related to functionality. In the shown examples of three enzymes of family 13, this 3D superposition is necessary to detect similarities and discrepancies between subfamilies of strict hydrolase and hydrolase-transferase. 

Figure 2 A global alignment of selected peptides from the thionin family reveals the similarities In their sequences. Increasing redness of the background Indicates higher scores, that Is, higher probability of the respective residue at that position (B Asp or Asn, Z Glu or Gin).

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