Gene 83
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-3bp overlap 
Selected Start Coordinate 
Selected Function 
HNH Endonuclease 
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 49507 has strength 3.686" 
Is there evidence for coding potential? 
Yes, there is evidence for coding potential. GeneMark S indicates intergenic coding potential. GeneMark displays some coding potential 
Both typical and atypical ps on GeneMarkS 
GeneMark shows decent coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando 83 (86 on phamerator) is conserved in the all of AU6.  
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? 
"Original Glimmer call @bp 49507 has strength 3.68" 
Does the start site have an associated ribosome binding site with a high score? 
The 49507 start site scores excellently.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start site leads to the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
No start sites conserved 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Weak start site conservation. Start of gene is divergent with Q3:S5 alignments frequently noted.  
BLASTp PhagesDB: Q3:S5 
BLASTp NCBI: Q3:S5 
BLASTp DNA Master: Q1:S1 
49507 is the start site 
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? 
Matches are strong, and these matches do align to proteins with functional assignments. Highest scoring match is to Uzumaki 84, an HNH endonuclease.  
PhagesDB BLASTp: e-value = e-111 
NCBI BLASTp: e-value =  3e-129 
DNA Master BLASTp: e-value = 0.0 
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? 
Quality match to HNH endonuclease domain. HNH observed in first domain. Three total HNH endonuclease catalytic domains observed. All allign to IU3E_M 
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 in phamerator is quite divergent towards the end of the AU6 subcluster. As such, it is difficult to assign functional assignment to this region.  
Is the proposed function found on the SEA-PHAGES approved function list? 
HNH Endonuclease 