Purpose and Rationale: Annotate Phage NapoleonB

Procedure:

• Downloaded the NapoleonB fasta file
• Auto-annotated NapoleonB in DNA Master

• Began with Gene 73
• Confirmed called start and spot with Glimmer and Genemark, and RBS computations
• Compared coding potential to Genemark Heuristics map. Gene 73 has about 30 base pairs left without a start point, making it inaccessible
• the next step was to BLAST the amino acid structure in NCBI and PhagesDB
• Phagesdb had several hits, but none that had a defined function
• NCBI showed similar results, showing, for the most part, the same phages as in PhagesDB
• HHPred was able to place the protein in a family, but again the family had no function
• Without a function for the protein, there is no way to predict synteny
• Phamerator shows similar genes in similar places for phages in the same family as NapoleonB, all without known functions as well

Repeated all steps above with Genes 74, 75, and 76.

Upon Completion:

• Reviewed each gene and ensured everything was filled out properly
• Marked all four genes as complete in Phagenotes

Results: All four of my genes are annotated to the best of my ability. There isn’t a whole lot to do, because there are no similar genes that code for proteins with known functions. There are some interesting notes to take out of the information presented.

Observations:

• All four genes have no known function.
• The gaps separating the genes are very short, but they are all gaps. The longest gap is 24 base pairs.

From HHPred:

• The proteins coded by genes 73 and  74 were placed in the same family, but the family has no known function.
• The protein from gene 75 was also placed in a different family, and again in one without a known function
• Gene 76 codes for a protein, but there were not enough hits to place the protein in a family

Function:

• NCBI and PhagesDB were unable to locate any similar proteins with known functions for the proteins coded by genes 73-76
• No other method of prediction was able to determine any evidence of function
• Despite lack of function, these genes were highly similar to genes found in many other Arthrobacter phages, from across the eastern and central United States

Future Plans: I understand that there are a lot of people who are having more trouble completing their annotations than I am. I can either help take on excess genes, or begin proofreading through their annotations to ensure their accuracy. It all depends on what is needed at the beginning of next lab session.