Gene 17
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Hypothetical protein 
Annotation Decision 1 (Is this a gene?): 
Gathering Evidence 
Explain Your Rationale 
Was the gene called by an auto-annotation program (Glimmer, GeneMark) 
Called by both 
"Original Glimmer call @bp 12579 has strength 3.52" 
Is there evidence for coding potential? 
Yes, there is strong evidence as indicated by both programs.  
GeneMarkS indicates both second and fourth order coding potential (typical and aytpical ps) 
GeneMark additionally indicates coding potential but to a lesser degree than that of GeneMarkS. GeneMark still indicates the presence of a gene.  
Is the gene present in other annotated genomes? 
Yes Lewando_17 (on phamerator 19) is conserved in GantcherGoblin and Uzumaki. This indicates that this is indeed a gene.  
Does the gene violate any of the major guiding principles? 
Yes, this is a gene 
Annotation Decision 2 (What is the best possible start site for this gene?): 
Gathering Evidence 
Explain Your Rationale 
What start site do Glimmer and GeneMark suggest? 
Both call at 12579 
"Original Glimmer call @bp 12579 has strength 3.52" 
Does the start site have an associated ribosome binding site with a high score? 
The 12579 site has an acceptable score, Z score of -2.207 and final score of -4.455, and the best score out of all possibile start site. This start site is supported due to the ability to produce an acceptable translation start site. 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes it results in the longest possible ORF - evidencing that this is the start site through maximizing coding potential.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, the 12579 start site is conserved in other genomes. In fact, it is the only conserved start site. This indicates that the 12579 start site is the start site as other phage genome suse the same start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, the start site is conserved in other phages as indicated by BLASTp. Specifically, the Lewando_17 genes has the same exact start site as other AU6 genes such as Uzumaki_14. The highest scoring match is from DNA Master where a score of 401 and e-value of 0 was attributed to the match tp Uzumaki_14.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:s1 
5769 is the start site. The next start site 5788 has a start site that has a excessively distant spacer distance for the Shine Dalgarno sequence.  
Annotation Decision 3 (What is the function of the putative protein?): 
Gathering Evidence 
Explain Your Rationale 
Does the protein align with a protein having functional assignment in BLASTp (phagesDB and/or GenBank) with an alignment of 10^-4 or smaller? 
Lewando_16 displays significant allignment to other phage proteins, however few of these proteins have assigned function. Once NCBI match has assigned function of that of a phosphoglycerol transferase which is not on the approved function list. 
PhagesDB BLAST: e-value = 6e-61 
NCBI BLAST:  e-value = 1e-47 
DNA Master BLAST:  e-value = 0 
Does this protein align with a protein having a functional assignment in the PDB or other database in HHPred with a probability of 90% or greater with appropriate coverage? 
No quality match on the standard databses:  
PHROGs produced some quality matches, to a potential translation factor and phage structural protiens. The match to phrog_3332 could be of interest, and indicates that that this protein is a phage tail protein.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Gene order conserved in AU6, as the Lewando_17 homologous in GantcherGoblin and Uzumaki are all flanked by major capsid and protease fusion protein upstream and tail terminator and major tail protein downstream. Ths indicated that this region plays a role in the assembly of Lewando. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 