Annotation of NapoleonB Part Two 2/13/2019

Rationale

The rationale behind these procedures is to start annotations on NapoleonB so that other research can be conducted.

Tools/Procedure

1. Previous DNA Master Annotations were loaded
2. Reading frames were examined (Genome > Frames> click “ORFS” button)
3. Gene locations were compared paying attention to gaps and overlap
4. NCBI was used to BLAST amino acid sequences against a large database of recorded sequences
5. Phages DB was used to BLAST amino acid sequences against the SEAPHAGES database
6. HHPred was used to compare the hypothetical protein structure against other hypothetical structures
7. Starterator and genemark were used to determine if the genes ought to be altered to include more or fewer base pairs
8. The information gathered was used to update phage notes

Results

Gene 65 – SSC:41757 – 41909, CP:Yes, SCS:Glimmer, ST:SA, BLAST-Start:Aligns with Arthrobacter phage Cheesy gp63 NCBI BLAST q1:s1 0.87 7E-22, Aligns with Arthrobacter Phage Cheesy gp63 PhagesDB BLAST q1:s1 1 7E-20, Gap:24bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 3.269 -2.511 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 66- SSC:41909 – 42091, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage Cheesy gp64 NCBI BLAST q1:s1 0.86 2E-24, Aligns with Arthrobacter Phage Kardesai gp65 PhagesDB BLAST q1:s1 1 4E-27, Gap:1bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.433 -4.402 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 67- SSC:42238 – 42366, CP:No No avaliable start codon, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage Mudcat gp62 NCBI BLAST q1:s1 1 3E-20, Aligns with Arthrobacter Phage Mudcat gp62 PhagesDB BLAST q1:s1 1 7E-17, Gap:146bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 3.269 -2.064 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 68- SSC:42368 – 42739, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Circum gp68 NCBI BLAST q1:s1 0.95 3E-76, Aligns with Arthrobacter Phage Kardesai gp67 PhagesDB BLAST q1:s1 0.97 8E-61, Gap:1bp gap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.433 -3.829 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Conclusion

There is very little information from which to draw conclusions about the data set; however, it appears that there is no known function for genes 65 through 68. As the rest of Napoleon B is annotated I will be able to draw more conclusions from the data.

Future Plans

In the future, I will continue my annotations of NapoleonB with the goal of being able to research my own questions once the gene is fully annotated.