Thus, nucleotide changes at position 274, Rigosertib ic50 Leucine (L) was changed to Valine (V). At position 340, Asparagine (N) was changed to Aspartic acid (D) while at position 391, Aspartic acid (D) was changed to Asparagine (N) and at position 436, Serine (S) was changed to Alanine
(A) (Table 5). The SIFT software was used to predict the effect of these changes with 41 homologous sequences fetched from the UniProt-SwissProt 56.6 database. Using SIFT, it predicts the possibility of the effect caused by the substitution change by using the scoring method. The score is the normalized probability that the amino acid change is tolerated. The reliability of this score is supported by the value, which measures the diversity of the sequences in the alignment. Generally, the substitution site of the score less than 0.05 is predicted as a deleterious site with the support of median conservation values between 2.75 and 3.25 considered as a reliable prediction. Our results showed that all substitution changes were tolerated to the alteration of the protein function with all prediction scores > 0.05 and supported by the median conservation value of 3.08 Transmembrane Transporters inhibitor (Table 5). Table 4 The genetic divergence of assemblages A and B Assemblage Nucleotide divergence (%) Ks Ka A 0.96 0.0019 -a B 6.76 0.039 0.001 Ks; divergence at synonymous
positions, Ka; divergence at nonsynonymous positions;ano nonsynonymous change Table 5 Score and median conservation values from the prediction Histone demethylase of the effect of amino acid substitutions Positions Substitution Changes Score Median conservation 274 Leu to Val 0.34 3.08 340 Asn to Asp 0.11 3.08 391
Asp to Asn 0.1 3.08 436 Ser to Ala 1.0 3.08 Since the low genetic variation level of assemblage A does not reach the usual value observed in sexual populations, almost identical nucleotide sequences do not warrant further analysis. Thus, the sequence data of assemblage A were not included in the downstream analysis. Estimate of geographic differentiation Phylogenetic https://www.selleckchem.com/products/gs-9973.html analysis has shown that both assemblage A and B isolates have been dispersed throughout all studied geographical locations and appeared to be weakly supported for geographical sub-structuring. To determine if the traits from this inference were correct, the level of genetic distinction between each geographic population was estimated. The Wright’s test measures the level of genetic distinction between populations, representing with fixation index (F ST) value from 0 to 1. A value of zero indicates no divergence and implies that two populations are freely spread whereas the positive deviation from zero indicates the extent of genetic differences. A value of one would imply that two populations are completely separate. The estimated values showed little difference between each pair of the three regions and no significant differences were exhibited (Table 6).