Gene 6
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Hypothetical function 
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 Glimmer and GeneMark 
"Original Glimmer call @bp 2667 has strength 5.31" 
Is there evidence for coding potential? 
Yes, in GeneMarkS coding potential as can be seen in the image below. Genemark also displays coding potential. 
Is the gene present in other annotated genomes? 
Yes, Uzumaki (6), Zeina (6), and Gantchergoblin (5) are homologous to Lewando (7) Gene 6.  
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 2667, score of 5.31 
"Original Glimmer call @bp 2667 has strength 5.31" 
Does the start site have an associated ribosome binding site with a high score? 
No, the 2667 site has quite a low Z score (worst) and final score (worst). This may be again due to co-transcriptional regulation.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, not the longest ORF. Other longer ORFs would not necessarily produce excessive overlaps. This does not support that 2667 is the start site. 
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, however the 2661 start site is far more conserved though. Overall this does not support the 2667 start site call. 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes. BLASTp indicates that this is indeed the start site for said gene, as indicated by start site conservation, query cover, and homology in other AU6 subcluster genes. 
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:1 
2667 is the start site, as demonstrated by the conservation with the other phages in the AU6 subcluster.  
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? 
Yes, Lewando_6 alligns well with other charecterized hage protiens, although these proteins do not have any short of function attacked. The DNAmaster match had a score of 607, which indicates a significant allignment between Lewando_6 and Uzumaki_6.  
PhagesDB BLAST: e-value = 1e-67 
NCBI BLAST:  e-value = 0 
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? 
With the standard set of matches, there were no quality matches. The highest scoring match was a match to " 
Phage_connect_1 ; Phage gp6-like head-tail connector protein" which had a probability of 70.91 and E-value of 30.  
When using phrogs, though, other high scoring matches were found. The highesy scoring match with function on the phage protein approved functions list was a head-tail connector protein, which had a probability of 99.78 and a E value of 2.3e-18.  This match had a score of 122.3. 
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Yes, this gene is in an ordered region of the genome insofar that the gene order in this region is similair throughout AU6. However due to the significant proportion of proteins that are uncharecterized, it is difficult to attribute the function of this region.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical function 