Percentage sequence identity

If the percentage sequence identity between the structure and die sequence to be modeled Is well below 50%, then the quality of the sequence alignment is the... 

Figure 2.2. Pairwise percentage sequence identity for 33 cupredoxins plotted against (A) hydrophobic MIF similarity index and (B) electrostatic potential similarity index. The linear regression correlation coefficients...

Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family.

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

To assist the interpretation of family memberships, overall probability scores for both global and motif matches are provided for top hit families. The global score is computed from the BLAST e-value, the SSEARCH score, and the percentage of sequence identity at overlapped length ratio in SSEARCH alignment. The motif score is computed from the ratio of mismatched amino acids to ProSite patterns, and the hidden Markov motif match score. Family information from ProClass, with hypertext links to all other major family... 

Interpreting the score. Suppose that the sequences of two proteins each with 200 amino acids are aligned and that the percentage of identical residues has been calculated. How would you interpret each of the following results in regard to the possible divergence of the two proteins from a common ancestor ... 

A relatively complete listing of primary sequences for the iLBP family is presented in the top portion of Table III a smaller version is given in the bottom portion. The latter contains the amino acid sequence numbers for two of the subfamilies and is included to make it easier for the reader to find residues that will be specifically referred to in subsequent discussions. In Table III, elements of secondary structure, based on comparisons of several structures, are also indicated. In addition, the levels of sequence identity are presented as percentages in Table IV. They have been tabulated using an average iLBP length of 132 amino acids. 

FIGURE 3.2 Techniques used for sequence- and structure-based function assignment and their relationship to percentage of sequence identity between the query protein and observed matches. 

The value of A, in turn, is exponentially related to the percentage of identical core residues so that a protein structure will conservatively provide a close general stmctural model for other proteins if the sequence similarity exceeds 50%. Consequently, there is an increasing use of this type of relationship to predict tertiary stmcture and secondary elements from primary sequences. Nevertheless, there are cases, such as the Lactobacillus casei and E. coli dihydrofolate reductases, where the primary sequence similarity is only 30% yet A is only 1.3 A (727). 

Table 15-1 Percentage amino acid sequence identities (excluding gaps) of aligned sequences of ferritins and rubrerythrin...

Once the basis set has been identified, the next task is alignment of the target sequence to these known structures or structure this lies at the heart of comparative modelling and is still the most frequent and serious source of errors. While the correct sequence alignment is trivial if the percentage identity between compared sequences is high (say 35%), it becomes extremely difficult when sequence identity is low (25% or below). 

Number of actives is given as A. Enrichment factors are calculated at the given percentage of the ranked database. Abbreviations sequence identity (seq. id.), data not available (NA), molecular weight (MW), topological polar surface area (TPSA), number of actives confirmed experimentally (A). Hit rate (given in %) was defined as the ratio ofAtothe number of compounds tested experimentally. 

Sequence identities are in parentheses. Enrichment factors are calculated at (%) percentage of the ranked database. Enrichment factors obtained by holo structures were used from Ref. [48]. 

For the sequences shovm, there are 27 identities and 2 gaps (over a total length of 98 residues in sequence 2). Based on a score of -I-IO for an identity and -25 for a gap, the score would be 270 - 50 = 220. The percentage of identical residues can be calculated as 27/98 = 27.6%. One could also note that the % identity is higher over the first 75 residues (26/75 = 34.7%). Based on the methods of sequence shuffling and statistical comparison (Figures 7.7 and 7.8), one can comfortably conclude that these scores are statistically significant. 

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