NapoleonB Gene 25 (2/11/19)
Rationale:
Start annotating NapoleonB. Once NapoleonB fully genome is annotated, the process of brainstorming research questions about NapoleonB can begin.
Tools:
- DNA Master
- NCBI
- PhagesDB
- GeneMark
- HHPred
- Phamerator
- phage notes
Procedure:
- Auto-annotated NapoleonB FASTA file.
- Conducted a GeneMark on NapoleonB.
- Determined the stop and start with the highest coding potential for gene 25 based off the “Choose ORF Start” window and the GeneMark.
- Performed a HHPred search on NapoleonB gene 25.
- BLAST was performed on NapoleonB gene 25 through both NCBI and PhagesDB.
- Annotated NapoleonB gene 25.
Results:
The following image shows NapoleonB gene 25’s annotation.
The following images were examined to determine whether or not there was enough supporting evidence for a function.
HHPred Results
NCBI BLAST Results
CDD Results
BLAST PhagesDB Results
Phamerator Comparison
Conclusion:
A difficult call occurred when determining whether or not there was enough supporting evidence for gene 25 to have a function. HHPred called a holin function with a 99.92 probability. CDD also called the holin function. Both BLAST results showed a low percent alignment, but the E-values were acceptable. On Phamerator, none of the other AM cluster genes have the holin function labeled on them. Gene 25 was annotated with the holin function.
Future Work:
Annotate NapoleonB genes 26-28.
