Gene 13
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 7761 has strength 13.59 
Is there evidence for coding potential? 
Yes, there is strong evidence as indicated by GeneMarkS - pictured below.  Genemark showscoding potential.  
Is the gene present in other annotated genomes? 
No - as indicated by phamerator. Lewando gene 13 (15) is not conserved in the AU6 subcluster. 
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 7761, with high strength 
"Original Glimmer call @bp 7761 has strength 13.59" 
Does the start site have an associated ribosome binding site with a high score? 
7761 has a solid Z and final score. The top scoring start site was downstream to the 7761bp start site, at n[ 7902. Overall, the 7761 start site is evidenced sufficiently. 
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 - which suggests that 7761 is indeed the start site.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 7761 start site is the most conserved start site, indicating that this is indeed the start site for this gene.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Not really – does not align very well to other proteins (best query alignment is 9-5 match with Sporto_8) 
BlastP PhagesDB: Q1:S1. To note, the best match whar a Q2:S3 allignment, but numerous other proteins allligned 1:1.  
BlastP NCBI: Q2:S3 
BlastP DNA Master: Q2:S3 
7761 is the start site. Although the most homologous proteins have a start site 2 bases further downstream, that start site is not available for Lewando_13.  
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_13 displays sequence simiairty to may othr phage protieins, unfortunately though, these proteins do not hav a functional assignmt, eveb the lesser degree matches. The highest scoring matchup is to SPORTO_12  in DNA, with a score of 475.  
PhagesDB BLAST: e-value = 1e-104 
NCBI BLAST:  e-value = 1e-74 
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 
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
The gene order in this region is somewhat conserved - with the downstream portal protein conserved throughout AU6. There is little upstream conversation between Lewando and the rest of AU6. Given the presence of upstream structural proteins, this protein may also hold structural function.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 
> 