The Hop2 and Mnd1 families

The orthologous groups of Hop2 as well as Mnd1 proteins are well defined in public ortholog databases (OrthoMCL-DB) and family collections (Pfam). Using the full length Hop2 and Mnd1 sequences extracted from these resources, a common core domain architecture can been defined for these protein families. In the two independently analyzed protein sets, highest conservation is observed in a segment of approximately 70-80 amino-acids (aa) typically found in the very N-terminus of the proteins. A 60-80 aa long region with a high likelihood of forming coiled-coil structures is found adjacent to the conserved domains in Hop2 as well as Mnd1 proteins (known to be involved in hetero-dimerization with Mnd1 and potential homo-dimerization: 17426123). A shorter C-terminal segment with a high helical content follows (required for efficient DNA binding: 15192114).

Hop2p and Mnd1p in Tetrahymena

Hop2 and Mnd1 protein families are typically represented by one member per species. Unexpectedly, two Hop2 and two Mnd1 proteins are found when applying profile hidden Markov models (HMM) against the Tetrahymena proteome (using the HMMER 2 package, Sean Eddy,

Hop2p and Mnd1p show distant sequence similarity

Using sensitive sequence analysis techniques, we find a distant similarity of the Hop2 protein family to the Mnd1 protein family:

The Hop2-Mnd1 conserved domain

The likely homologous N-terminal conserved domain of Hop2 and Mnd1 proteins is predicted to belong to the "winged helix" DNA-binding domain superfamily. One among several approaches to illustrate the similarity is depicted here: