Annotation of gene 77~80 & *99 2.11.19
Rationale:
To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. PhageNotes is also introduced as a convenient way to annotate genes and revising them.
Materials:
- Laptop
- DNA Mastering Program
- Gene sequence of phage NapoleonB
Procedure:
- Opened and auto-annotated the fasta file of NapoleonB downloaded from Phagesdb.
- Assigned genes were 77-80 & *99
- The genome sequence were uploaded to genemark to look more coding potential.
- The starterator on Phagesdb were found and considered.
- gene product sequence were then Blasted on NCBI pBlast, Phagesdb pBlast, HHpred, NCBI CDD.
- Looked for SIF-syn on Phamerator.
Results/Next Steps:
Gene 77:
SSC: 45552, 46064 CP: no SCS: Both ST:NI BLAST-Start: Arthrobacter phage Mudcat, 72, NCBI, Q1:S1, 99%, 6e-120 Gap:100 bp LO:yes RBS: Kibler7, Karlin medium, 2.442, -3.794, no F: HNH endonuclease SIF-BLAST: HNH endonuclease, NCBI, Arthrobacter phage Mudcat, 72, YP_009300761.1, 99%, 6e-120 SIF-HHPred: HNH endonuclease, NA, PF13392.6, 98%, 99.25%
Gene 78:
SSC: 46030, 46338 CP: yes SCS: Glimmer ST: NI BLAST-Start: Arthrobacter phage Mudcat, 73, NCBI, Q19:S1, 81%, 4e-52 Gap: overlap 35 LO: yes RBS: Kibler7, Karlin medium, 1.462, -5.943, no F: NKF SIF-BLAST: NKF (Hypothrtical protein) SIF-HHPred: NKF (Probability lower than 90%)
Gene 79:
SSC: 46338, 46625 CP: yes SCS: Both ST: SS BLAST-Start: Arthrobacter phage SEA ARCADIA, 78, NCBI, Q1:S1, 98%, 2e-64 Gap: 1 LO: yes RBS: Kibler7, Karlin medium, 3.160, -3.263, no F: SIF-BLAST: NKF SIF-HHPred: NKF
Gene 80:
SSC: 46626, 46757 CP: yes SCS: Glimmer ST: NI BLAST-Start: Arthrobacter phage KEANEYLIN, 75, NCBI, Q1:S1, 100%, 6e-21 Gap:0 LO: yes RBS: Kibler7, Karlin medium, 1.689, -6.149, yes F: NKF SIF-BLAST: NKF SIF-HHPred: NKF
Gene *99:
SSC: 57534, 57791 CP: yes SCS: Both ST: SS BLAST-Start: Arthrobacter phage Circum, 99, NCBI, Q1:S1, 98%, 9e-57 Gap: 11 LO: yes RBS: Kibler7, Karlin medium, 3.012, -3.054, no F: NKF SIF-BLAST: NKF SIF-HHPred: NKF
In the next lab, some of the problems regarding the genes would be addressed.