2/15/19

Rational:

To annotate genes 11 and 12 for NapoleonB and enter them in PhageNotes

Procedure:

• Dowloaded the fastA and auto-annotated NapoleonB
• Entered the gene call after genes 11, 12 and 98 in the home tab for PhageNotes
• Opened the genemark for NapleonB
• Checked to see if the coding potential was covered by the current start and that it was the ongest ORF
• Entered the start and stop codon
• Entered who the start was call and chosen by
• Checked phagesdb to see whether the gene’s start matches with the most called start (starterator)
• BLASTed genes 11 and 12 through NBCI and Phagesdb
• Ran the genes through HHpred
• Entered the required information for the NBCI and phagesdb hit in PhageNotes
• Calculated the gap/overlap for the gene and its upstream gene
• Selected the gene to get the information needed for RBS
• Entered the information for the hits in NBCI (BLAST and CDD), Phagesdb, and HHpred for the function
• BLASTed the surrounding genes and looked at Phamarator to look for for SIF-Syn

Observations:

• The genemark showed that the current start does not cover the coding potential for gene 11, but it is the LORF
• The coding potential is covered for gene 12 and it was the LORF
• Both genes were LORF
• Gene 12 had a gap of more than 10 bp
• Genes 11 and 12 both agreed with the starterator
• For gene 11 the NBCI hit was Arcadia and phagesdb was Xenomorph
• For gene 12 the NBCI hit was Arcadia and phagesdb was Xenomorph
• Gene 11 had a overlap of 17 and gene 12 had an gap of 19
• For both genes the SD score for the chosen start was not the best
• The funtion for genes 11 and 12 is capsid maturation protease, however this was only supported by the NBCI BLAST for both genes

Fig.3 – The teal block shows gene 11 and the yellow and green blocks representing genes 10 and 12 for the phage KeanyLin do not show signs of synteny as they do not match the function of the genes 10 and 12 in NapoleonB.

Conclusion:
The genes 11 and 12 were finished and their function was found to likely be a a capsid maturation protease for both. Note the only source that supported this was the NBCI BLAST the Phagesdb, Phamerator, and HHpred did not. Next lab I will finish the annotation of  98 and help check any mistakes made.