SIAS (Sequence Identities and Similarities) Results for D1 domain in 9 Primate Species

An aligned translated sequence of only the D1 domain of CD4 in the 9 primate species was used. The sequence was aligned with MUSCLE and trimmed in AliView. The HMMSCAN results were used to decide where the D1 domain is located in CD4. SIAS calculated pairwise sequence identity and similarity with the inputed data. The left figure is the percent identity match between the primate species. The right figure is the percent similarity match between the primate species. Percent identity is based on exact amino acids that are shared between species and similarity identity is based on amino acids that share the same side chain chemistry. In both figures, the yellow highlights show the percent identity between the two macaque species (CD4-Macaca) with the Sumatran orangutan (CD4-Pongo). The red highlights show the percent identity between the Sumatran orangutan (CD4-Pongo) and the Sooty mangabey (CD4-Cercocebus), Golden snub-nosed monkey (CD4-Rhinopithecus), and Vervet monkey (CD4-Chlorocebus). The two macaques and the Sumatran orangutan make up the SIV-susceptible group and share a 93.68% percent identity and similarity in the D1 domain. The Sumatran orangutan share a decreased percent identity and similarity in the D1 domain with the Sooty mangabey, Golden snub-nosed monkey, and the Vervet monkey, which are a part of the SIV-resistant group. According to our phylogenies, Sumatran orangutans are more related to Sooty mangabey, Golden snub-nosed monkey, and the Vervet monkey, than to the macaques, indicating possible selection to differentiate the two groups. <br><br>