Rationale: Since Arcadia’s genome is already full annotated I’m using it as an  example genome for studying this group of genes. I’m going  to be figuring out if there are any interactions between these proteins to give insight on their function.

Tools: RaptorX Structure Predict, RaptorX DeepAlign, Jmol, TMHMM

Procedure:

1. Ran the protein  sequence of  Arcadia’s genes 59-61 through the  structure prediction tool of RaptorX to discover what the protein products of the genes would look  like structurally.
2. Ran different combinations of each protein product with each other to see if there is a possibility of the genes interacting with each other using DeepAlign.
3. Visually looked  at each protein product using Jmol and found that gene 59 looks like a transmembrane protein.
4. Ran the protein sequence through TMHMM and found that it is in fact a transmembrance protein.
5. Ran TMHMM for other proteins of members of the supergroup with pham 19129.

Results: DeepAlign results were >.3 therefore there is a greater than 90% probability that there are no interactions between these three proteins.

TMHMM for KeaneyLin

Conclusions and Next Steps: Most likely the proteins don’t interact with each other. However, most of the proteins all seem to be transmembrane proteins so their might be more to look in to there. This protein also seems to be a determining factor of which cluster the phage is in. I will continue looking in to interactions by visually comparing the DNA polymerase and the gene before it with proteins that normally interact with DNA polymerase or replication in general.