1. Bacillus Phage Annotation Phage Lab II, Spring 2015

2. Complete annotation of other phages, explore those genomes Nemo (Sathya & Molly) Claudi (Demetrius)Jugalone (Herleen) Zuko(Sailasya) DIGNKC (Ryan) + Didn’t annotate yet

3. CharacteristicPhrodoJugaloneZukoDIGNKCClaudi Best Blast Match Troll MegatronHakunaMG-B1 % Query Cover 9496919233 % Identity9899888774 % GC37.8 38.638.730.3 Genome Length, bp 16444316422716334516155226504 # predicted ORFs 288293296 48 # predicted tRNAs 00330 Genomic Comparison of VCU’s 2014-2015 Bacillus Phages

4. Phage# Predicted ORFs # tRNAs# ORFS with Functional Annotation/ % of total # of novel genes Zuko2963372 Vinny2747601 SageFayge3020700 Phrodo2880622 NotTheCreek2970480 NIgalana3020431 Jugalone2930560 DIGNKC a 296347- Claudi480 16

5. Dihydrofolate reductase Dephospho – CoA kinase Thymidylate synthase PhoH Endolysin Terminase HTH binding protein RecA Metalloprotease Exonuclease II Exonuclease I DNA Primase dUTP nucleotidylhydrolase Holiday junction resolvase Ribonucleotide diphosphate reductase alpha subunit Ribonucleotide diphosphate reductase beta subunit Flavodoxin Thioredoxin DNA Binding protein DNA Binding Protein Portal Prohead Protease Major Capsid Protein Tail Sheath Tail Assembly Chaperone RNA Helicase Tail spike Ligase Peptidase RNA Ligase Tail assembly chaperone HNH Endonuclease HNH Homing Endonuclease Tail assembly chaperone Ftsk/ SpoIIIE Protein HNH Homing Endonuclease ParM Metal Dependent Hydrolase Tape measure, tail lysin DNA Binding Protein Tail lysin 1 Tail fiber protein Minor tail protein Sigma Factor Baseplate assembly protein Methyltransferase Baseplate protein J Transposase DNA Helicase 2 HNH endonuclease III DNA Polymerase 1 HTH binding domain protein Exopolyphosphatase Holin HNH Homing Endonuclease Sigma Factor RecA ssDNA Binding Protein DNA Polymerase II DNA Polymerase 1 Functional Annotations for Bacillus Phage Phrodo Functional annotation for 62 proteins, (62/288)*100 = a little over 21%

6. What are the differences in Jugalone and Phrodo? Jugalone vs. Phrodo 17 protein phams in Phrodo that aren’t in Jugalone 3 are homing endonucleases 20 protein phams in Jugalone that aren’t in Phrodo DNA Primase dUTP nucleotidylhydrolase 229 genes: same gene length in Phrodo and Jugalone. 39 genes in Phrodo and Jugalone have the same function and exact gene length.

7. How as Phrodo 106 inserted, and what does it do? Novel Gene Gene 106 encodes for an HNH Endonuclease III protein. Located between gene 105 which codes for DNA Helicase II and gene 107 which codes for an HTH Binding Domain Protein Gene 106 was inserted into Phrodo through an illegitimate recombination process (no overlap in purple shading.)

8. Can you determine how gene 114 was inserted into Jugalone? Matches Hmu1 HNH endonuclease Non bastille HNH endonuclease Non intron space on either side of gene 114, or non coding space Intron-mediated recombination

9. Are Jugalone 218 and 221 are transcribed? Phrodo 214, 217 and 219 ?

10. Yes, transcribed in reverse direction 214: SD 504 217: SD 273 219: SD 567

11. Is there a missing gene in between Jugalone gp 138 and 139? There is 261 bp gap between both genes. A gene with starting codon 97791 and stop codon 97920 was found Coding potential of the gene is too low, so it should not be added

12. Coding Potential Phrodo SD: 567 Jugalone SD: 609