2/11/19

Rational:

To start annotating the assigned genes 9-12 and 98 for NapoleonB and enter them in PhageNotes

Procedure:

• Dowloaded the fastA and auto-annotated NapoleonB
• Entered the gene call after genes 9 and 10 in the home tab for PhageNotes
• Downloaded 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 9 and 10 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 to look for for SIF-Syn

Observations:

• The genemark showed that the current start covers all the coding potential for genes 9 and 10
• Both genes were LORF
• Gene 9 had a gap of more than 10 bp
• Genes 9 and 10 both agreed with the starterator
• For gene 9 the NBCI hit was Arcadia and phagesdb was Tribby
• For gene 10 the NBCI hit was Mudcat and phagesdb was Xenomorph
• Gene 9 had a gap of 14 and gene 10 had an overlap of 4
• For both genes the SD score for the chosen start was the best
• The funtion for gene 9 was portal protein and gene 10 was hydrolase

Conclusion:

The genes 9 and 10 were finished and there function were found to likely be a portal protein and a hydrolase repectively. Note the only source that supported gene 10 as a hydrolase was a more specific type of hydrolase. Next lab I will finish the annotation of 11, 12, and 98.