Date of Award

Spring 2009

Degree Type

Thesis - Restricted

Degree Name

Master of Science (MS)


Mathematics, Statistics and Computer Science

First Advisor

Struble, Craig A.

Second Advisor

Lei, Ming

Third Advisor

Merrill, Stephen


Histone deacetylase 2-FKS06 binding proteins share two well-defined structural domains: the HD2 domain and the FKS06-binding domain. The evolutionary history of this protein family remains largely unknown. In this study, I examined phylogenetic relationships of members of the family using the Hidden Markov models CHMMs) that explain the similarities in the amino acid sequence. These HMMs were used to construct multiple sequence alignments and phylogenetic trees based on both the amino acid sequence of the entire proteins, and both the HD2 and the FKBP domains. The multiple sequence alignments and the phylogenetic trees show that similarities in phylogenetic relationship of the proteins in the family on two levels. These levels are the entire protein sequence and on level of both the domains, the HD2 domain and FKBP domain. These species are distributed through eukaryotes, being found in fungus, insects and plants. Phylogenetic analysis of these alignments suggests that both domains evolved together and all HD2-FKBP proteins evolved from a common ancestor. The goal of this project is to identify additional species that have proteins belonging to the HD2- FKBP family to show the evolutionary relationship between these proteins by comparing multiple sequence alignments and phylogenetic trees of the entire protein and each of the two domains. The domains were extracted using hidden Markov models of the domains. In order to extract the HD2 domain, a hidden Markov model of the domain was created. Using the hidden Markov models for the HD2 domain and the FKBP domain 39 new proteins from 24 new species were identified. In addition to fungus, insects, and higher plants which were previously classified as having proteins in this family, purple sea urchins and slime molds were added to the groups known to have proteins that belong to this family.