Gene 7
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) 
Yes, called by both Glimmer and GeneMark. To note, the start sites were different for both programs. This suggests that the start sites should be further examined, but that there is likely a gene in this region. 
"Original Glimmer call @bp 3011 has strength 7.65; GeneMark calls start at 3059" 
Is there evidence for coding potential? 
Glimmer call strength: 10.55  
GeneMarkS shows coding potential in this region as well. This is shown below.  Genemark also displays coding potential.  
Is the gene present in other annotated genomes? 
BLASTp match to a terminase protein in phage Zeina. 100% query cover, 0.0 E value, and 94.28% E value. To note, Zeina is another phage in. the AU6 subcluster. In phamerator, Lewando gene 7 (8 in phamerator) aligns to gene 7 (7) in Zeina.  
Does the gene violate any of the major guiding principles? 
No, there is a substantial (27bp) but not prohibited (>30bp) overlap with Gene 6. There is a small non-coding gap at the 5' end of the gene that spans 17bp, but otherwise is closely packed in. The gene is >120 bp (Gene 7 is 513bp). This gene does end with a stop codon. This gene starts with a start codon as well.  
Yes, gene 7 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? 
Glimmer call at 3011, GeneMark called at GeneMark calls at 3059 
"Original Glimmer call @bp 3011 has strength 7.65; GeneMark calls start at 3059" 
Does the start site have an associated ribosome binding site with a high score? 
The 3011 start site is a highyl scored start site (for z and final scores). This suggests that the 3011 site is a potential start site. The 3059 start site has a better final score, and also deserves consideration.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, but upstream start sites would result in excessive overlap, making them inviable as start sites. 
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, 10 matching start sites for 3011. There is further support for the 3059 start site (27 MA), however the 3059 start site would decrease the coding potential for this Lewando_7.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Full query cover against Zeina with the 3011 start site, so yes. This conservation in start sites and query cover indicate that the correct start site was picked. To note, there are some gaps with respect to the Zeina and Lewando genes.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:1 
3011 is the start site, due to the increase in coding potential, and its conservation in start site within other phages in the AU6 subcluster. Note: Rish called the start site at 3059. 
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_7 does allign with other charecterized phage protiens, although these proteins do not have dfined funvtion. The DNAmaster match had a score of 594. This match was against Zeina_7, a hypothetical protein.   
PhagesDB BLAST: e-value = 1e-92 
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? 
All matches had low scores and excessive E values.  
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, gene order in this region is conerved. Here Gene 7 is labelled as 8. Many proteins in this region have function that is undefined.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical Protein 