Rationale

Start performing annotations on NapoleonB to understand certain functions for genes and provide further research to be conducted afterwards.

Procedure

1. Opened DNA master with NapoleonB FASTA file
2. Opened DNA –> Frames –> ORF —> RBS (for genes 89-92)
3. Blasted each genes’ products on NCBI, phagesdb, HHPred, and DNA master for preparation
4. Filled out template for each gene using information from above listed sites
5. Opened gene mark for genes 89-92 and phamerator
6. Saved as new file and uploaded findings on class google sheets

Observations/Results

Gene 89

Original Glimmer call @bp 51379 has strength 12.26
SSC:51379,51708 CP:yes SCS:both ST:SS BLAST-Start:Xenomorph_Draft,83,phagesdb,query 1 to subject 1,100,7e-62 Gap:1 LO:NA RBS:Kibler7,Karlin Medium,2.290,-5.154,no F:NKF SIF-BLAST:NKF,Circum_88,ALY08771.1,99%,2e-73 SIF-HHPred:Signal transduction histidine kinase,COG,COG4585,COG4585,100%,87.68 SIF-Syn:NKF

Gene 90

Original Glimmer call @bp 51709 has strength 6.33
SSC:51709,51894 CP:yes SCS:both ST:SS BLAST-Start:Xenomorph_draft,84,phagesdb,query 1 to sequence 1,96,7e-28 Gap:0 LO:NA RBS:Kbler7,Karlin Medium,3.023,-2.566,no F:NKF SIF-BLAST:NKF,Sea_Arcadia_87,ASR80050.1,93.55%3e-35 SIF-HHPred:ribosomal protein L20A (L18A),COG,RPL20A,COG2157,73%,91.48 SIF-Syn:NKF

Gene 91

Original Glimmer call @bp 51891 has strength 7.86
SSC:51891,52247 CP:yes SCS:both ST:SS BLAST-Start:Nason,88,phagesdb,query 1 to sequence 1,95,2e-65 Gap:4 LO:NA RBS:Kibler7,Karline Medium,2.546,-3.590,no F:NKF SIF-BLAST:NKF,Sea_Arcadia_88,ASR80051.1,94.92%,4e-78 SIF-HHPred:FG-GAP repeat,FG-GAP,PF01839.23,34%56.96 SIF-Syn:NKF

Gene 92

Original Glimmer call @bp 52247 has strength 7.98
SSC:52247,52492 CP:yes SCS:both ST:SS BLAST-Start:Xenomorph_draft,86,phagesdb,query 1 to sequence 1,100,2e-41 Gap:1 LO:NA RBS:Kibler7,Karlin Medium,3.269,-2.064,no F:NKF SIF-BLAST:NKF,Mudcat_86,YP_009300775.1,93,67%,1e-48 SIF-HHPred:Agrobacterium tumefaciens protein,Atu,Atu4866,PF11512.8,93%,70.95 SIF-Syn:NKF

For all genes, there wasn’t a huge gap or overlap of >10 bps. All gaps/overlaps ranges from 0-4 bps. I did not had to correct the ORF or start codon as I agreed with starterator for all genes. All genes had NCBI, phagesdb, and DNA master Blast state “hypothetical protein” or “unknown function.” However, HHPred had its functions stated. I made the call that none of the genes had a functions. Also, none of the genes had a conserved domain provided, so on the google sheet CDD was filled out as “no.” Two of the genes after BLAST compared itself to NapoleonB_draft, so I chose to use the BLAST data with the one right below NapoleonB_draft.

Next Steps

Continue with the annotation of the current genes that were assigned to me and edit them along the way. Also to apply the knowledge for future research and presentation.