Nd of average amino sequences The difference full-length protein acid …

Nd of average amino sequences The difference full-length protein acid composition between The difference of average amino acid composition between indel sites and full-length protein sequences. The y-axis shows the natural logarithm of the ratio of average amino acid frequency in the indel sites to that in the fulllength protein sequences. Figure 4 A 3D view of an indel site by the Jmol applet on Indel PDB A 3D view of an indel site by the Jmol applet on Indel PDB. The indel site (insertion) is 14 amino acid long, present on a query protein, 1EDO_A (Beta-keto acyl carrier protein reductase), in an alignment with a subject protein, 1UZL_A (3-oxoacyl-[acyl-carrier protein] reductase). The indel site has an alpha-helix structure. length distribution models of indels can provide insights about indel abundance among related proteins.Sequence composition of indels The average sequence composition of the 20 amino acids in each of the 117,266 indel sites was calculated, and the calculation was repeated in the full-length sequences of the11,294 indel-containing proteins, where those indel sites were extracted from. Indels and their indel proteins were classified into four groups according to their length: indels with 1, 5, 10, 15, or 20 residues. Additional file 1 summarizes the sequence composition results and the corresponding chi-square and p values of each indel length category, by comparing indel sites and their indel-containing proteins. The average amino acid composition of indels with different minimal length is depicted in Figure 5. As shown in the Figure, the average residue percentages of A, D, and E increased, but those of G, L, N, S, T, and Y decreased when the length of indels went up. The rest of amino acids did not show any clear trend among different indel-length groups. This resultindicated that residues such as Alanine (A) and Glutamic acid (E), which prefer a helix conformation [27], are more frequently observed as the length of Capecitabine indels increased. This observation is supported by the later analysis of secondary structural composition, which showed an increase of alpha-helix content (H) in indels as length increased. Figure 6 shows the natural logarithm of the ratio of average amino acid frequency in the indel sites to that in the full-length protein sequences. Some trends can be easily identified from the Figure. For instance, indel sites contained more D, P, and Y in comparison to the entire protein sequences, while I, L, Q, T and V were reduced in indel sites. The differences are significant at P value PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17139194 amino acid composition between indel sites and loop sequences. The y-axis shows the natural logarithm of the ratio of average amino acid frequency in the indel sites to that in the loop sequences.Page 7 of(page number not for citation purposes)BMC Bioinformatics 2008, 9:http://w.