Sequence similarity/alignment

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. 

Fig. 4. Amino acid sequence of several histone HI proteins to illustrate the macroheterogeneity of linker histones. Amino acid sequence of two highly specialized development-specific members of the histone HI family. A. Oocyte specific mammalian histone Hlfo (previously Hloo) [116]. B. PL-I (EM-1/6) protein from the sperm of the razor clam Ensis minor [120]. These two sequences are shown in comparison to the highly specialized histone H5 from chicken erythrocytes. The regions corresponding to the trypsin-resistant (winged helix motif [96]) which is characteristic of the protein members of the histone HI family are indicated by a box and have been aligned to show the sequence similarity.

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