2.11.2019 Annotations of Gene 49 and 50 of NapoleonB

Rationale: Since the procedures and skills for annotating genomes had been developed through extensive practice with phage Elesar, annotations for Napoleon were finally ready to begin. Therefore, genes were assigned and genes 49 and 50 were annotated.

Tools/Procedure:

• DNA Master
• Starterator
• HHPred
• NCBI BLAST
• PhagesDB Blast
• Phamerator

1. Opened PhagesDB and found NapoleonB fasta file. Downloaded file
2. Auto-annotated NapoleonB on DNA Master
3. Opened ORF Screen
4. Began RBS value examination
5. Annotated genes 49 and 50

Results:

Gene 49-

Gene 50-

Phamerator that applied for both genes:

Gene 49: 

SSC:31823 – 32392, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Tribby gp48 NCBI BLAST q1:s1 0.99 3E-132, Aligns with Arthrobacter Phage Tribby gp48 PhagesDB BLAST q1:s1 0.98 e-100, Gap:15bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 2.684 -3.22 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF, upstream gene is NKF, downstream gene is NKF, just like in phage Nason

Gene 50: 

SSC:32516 – 32824, CP:No No ORF available would cover all of the potential, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Arcadia gp49 NCBI BLAST q1:s1 0.99 2E-65, Aligns with Arthrobacter Phage Nason gp49 PhagesDB BLAST q1:s1 0.98 e-50, Gap:123bp gap, LO:No, RBS:Kibbler7 and Karlin Medium 3.16 -2.293 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF, upstream gene is NKF, downstream gene is NKF, just like in phage Nason

Conclusions: Both of the genes annotated today had fairly straightforward decisions that were made. The questionable decisions came within the coding potential of gene 50 and the gap that preceded gene 50. There was a very slight amount of coding potential that extended past the earliest start codon of the gene, which resulted in the answer that was listed but there was deliberation on whether or not the amount of potential was considered to be significant. Furthermore, the gap between gene 49 and 50 is slightly longer than is normally seen when examining bacteriophage genomes, so there are some questions about whether or not there is a gene that was not detected by the auto annotation.

Next Steps: The gap between genes 49 and 50 will be examined, and genes 51 and 52 will be annotated during the next available lab time!