Aligned sequence

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. 

A sequence profile represents certain features in a set of aligned sequences. In particular, it gives... 

Aligned sequences of 16 members of the sugar transporter family. Residues which are identical in 5=50% of the 16 sugar-transporter sequences (excluding the quinate transporter (qa-y), the citrate transporter (CIT), the tetracycline transporter (pBR322) and lac permease (LacY)) are highlighted, and recorded below the sequences as CONSERVED . The locations of predicted membrane-spanning helices are indicated by horizontal bars. The sequences were taken from the references cited in the text. 

Fig. 5.2. E2 sequence alignments. Sequences of the twelve E2s found in the PDB. The active-site cysteine is colored green, identical residues colored red, and conserved residues colored blue.

Fig. 8. CDK4 selective library design process of Honma et al. (64). (A) Align sequences of 390 kinases. Dark circles denote residues with <40% conservation or subject to replacement in CDK1/2/6. (B) Darker residues in ATP binding site pinpoint the least conserved residues highlighted in (A). (C) Map lead structure onto difference residues. Arrows denote direction and distance to said amino acids. (D) Design library according to these constraints. Resulting compounds show up to 180-fold selectivity for CDK4 with respect to CDK2. Adapted from ref. 64.

Table 8.1 Percentage of identity between the aligned sequences of the ARs and those GPCRs for which crystallographic structures are available...

UCSC genome browser http //genome.ucsc.edu/cgi-bin/ hgGateway Visualization of aligned sequence reads in the genome of interest... 

The TIGR has software systems available for free download. These include software for gene finding/annotation, alignment, sequencing/finishing, and microarray analysis. All of them are OSI (Open Source Initiative) Certified Open Source Software. 

As you move the cursor pointing to amino acid residues of the aligned sequences in the Align window, the corresponding residues of the superimposed molecules in the Display window blink from blue to yellow, allowing an easy visualization of the overlap. In addition, the rms distance of the superimposed residues is displayed. 

Fig. 7. (A) Aligned, partial sequences of a number of calmodulin-binding peptides. The boxes indicate residues that are generally occupied by apolar residues. Reported dissociation constants for interaction with calmodulin are given on the right. LK2, A mode peptide VIP, vasoactive intestinal peptide GIP, gastric inhibitory peptide. (B) The mean hydropho-bicities for the residues at a given position were plotted versus their position in the aligned sequence. The horizontal bar indicates the period of an a helix. From Cox et al. (1985).

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