Purpose: The purpose of this lab is to finish annotations of NapoleonB’s genes.

Tools/Procedures:

Tools:

• DNA Master
• NCBI
• PhagesDB
• HHpred
• Phamerator

Procedures:

1. DNA Master, NCBI, PhagesDB, HHpred, and Phamerator were opened to begin annotations of genes 1-4 of NapoleonB.
2. Annotations were completed for genes 1-4 were completed using the tools listed above.
3. Work was saved and added to Phage Notes.

Results:

Gene 1

SSC:70 – 285, CP:No No start codon to cover all coding potential, SCS:Both, ST:SS, BLAST-Start:Aligns with circum gp1 NCBI BLAST q1:s1 98 5E-45, Aligns with Nason gp1 PhagesDB BLAST q1:s1 1 9E-36, Gap:first gene, LO:, RBS:Kibbler7 and Karlin Medium 2.601 -4.222 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 2

SSC:736 – 1083, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Mudcat gp3 NCBI BLAST q1:s1 0.99 3E-77, Aligns with Xenomorph draft gp2 PhagesDB BLAST q1:s1 1 6E-59, Gap:450bp gap, LO:No, RBS:Kibbler7 and Karlin Medium 2.765 -3.399 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 3

SSC:1076-1483, CP:No No start codon to cover all coding potential, SCS:Both, ST:SS, Blast-start: Aligns with Correa gp4 NCBI BLAST q1:s1 0.99 1E-96, Aligns with Tribby gp4 PhagesDB BLAST q1:s1 1 3E-77, Gap:8 overlap, LO:NA RBS:Kibler7 and Karlin Medium2.159 -5.634 No, F:HNH endonuclease, SIF-BLAST: HNH Endonuclease domain protein Supported by NCBI BLAST Correa gp4 ASR80065.1 0.99 1.00E-96, HNH Endonuclease domain protein Supported by PhagesDB BLAST Tribby gp4 NA 1 3.00E-77, SIF-HHPred:HNH endonuclease supported by COG gpNA COG3183 0.52 98.73, SIF-Syn:NKF

Gene 4

SSC:1506-2432 CP:Yes SCS:Both ST:SS Blast-start:Aligns with Circum gp5 NCBI BLAST q1:s1 0.99 0E+00, Aligns with KeaneyLin gp4 PhagesDB BLAST q1:s1 0.99 0E+00, Gap:22 gap, LO:Yes RBS:Kibler7,Karlin Medium 3.269 -2.511 No, F:endolysin, LysM-like, SIF-BLAST:endolysin Supported by NCBI BLAST Circum gp5 ASR80065.1 0.99 0, LysinA Supported by PhagesDB BLAST KeaneyLin gp4 NA 0.99 0, Peptidase Family M23 supported by a CD found from the Pfam databse  gpNA pfam01551 1.65E-22, SIF-HHPred:LysM supported by COG gpNA COG0739 0.41 99.36, SIF-Syn:NKF

Conclusions:
In conclusion, genes 3 and 4 were determined to have a function, HNH endonuclease and endolysin respectivly. Genes 1 and 2 were determined to have no known function, as none of the results from BLAST or HHpred yielded any known function for these genes. All of the assigned genes have now been completed.

Future Work:
Future work will include checking all annotations to make sure they are correct and accurately reflect the results found. Also, the gap between gene 1 and 2 will need to be checked more thoroughly to determine if a gene needs to be added.