Rationale: Purpose of the lab is to become familiar with PhagesNotes and to learn how to annotate tRNA’s.

Procedure:

• DNA Master was opened and Elesar FASTa file was opened and auto-annotated.
• NCBI was pulled up to blast genes 26,27,32 and 41.
• HHPred was opened up and databases COG_KOG_v1.0 and Pfam-A_v32.0 were set. Genes 26,27,32, and 41 were submitted into the databases to view common homology detection and structure prediction
• PhagesDB was opened and genes 26,27,32, and 41 were blasted and results were analyzed.
• NCBI Blastp was pulled up and genes were blasted to compare similarities.
• Annotations for Elesar genes 32 and 41 were entered into PhageNotes.
• Learned the concept behind how annotations of tRNA’s are done and how to analyze the results from Starterator
• Annotations for Elesar genes 26 and 27 were checked and corrected. DNA Master, NCBI, PhagesDB, and HHPred were used to annotate the two genes as well as genes 32 and 41.

Results:

The Genes information that was entered into phagenotes are shown below:

Gene 32

SCS: 23223 – 26093 FWD CP: Yes SCS: Both LO: No BLAST-Start (NCBI): Yes, hypothetical protein PBI_BRIDGETTE, 30, Q601:S62, 37%, 0.0 BLAST-Start (PhageDB): Yes, Ryan, 32, Q1:S1, 89%, e-169 Gap: 7 F: lipase, LipC-like RBS: -4.852, no, 2.117 SIF-BLAST (PhagesDB): No, mirror tail protein, ryan, 32, 89%, e-169 SIF-BLAST(NCBI): Yes, lipase, LiC-like, Bridgette, AYN57291.1, 81%, 0.0 SIF-BLAST(CDD): Yes, lipase, Pfam, N/A, pfam13472, 59%, 0.0 SIF-HHPred: No, general function prediction only, KOG, Outative Zn-Finger protein, KOG1777, 82%, 99.82

Gene 41

SCS: 3093 – 31219 FWD CP: Yes SCS: Both LO: no BLAST-Start (NCBI): Yes, Mycobacterium virus Brujita, 35, Q7: S2, 60%, 4e-13 BLAST-Start (PhageDB): No Gap: 108 F: Helix-turn-helix DNA binding protein RBS: -6.997, 0.897 no SIF BLAST (PhagesDB): yes NKF SIF-BLAST(NCBI): Yes, helix-turn-helix, mycrobacterium Brujita, N/A, YP002242018.1, 60%, 9e-13SIF-HHPRED: No, procin activator protein, PFAM, ProcinActivator, PF11112.8, 78%, 99

Conclusions:

Continue to practice annotating genes and understand the new databases introduced in the lab. Checking genes is a great way for more practice on how to correctly annotate genes. This will help in annotating NapoleonB. Learning how to use PhageNotes will be helpful in the future, and it organizes the annotations into one sheet.

Future:

Continue to learn more about annotations and to become familiar with the databases. It will help when it comes time to annotate NapoleonB.