Gene 88
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-3bp overlap 
Selected Start Coordinate 
Selected Function 
Helix-Turn-Helix DNA Binding 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 52023 has strength 8.38" 
Is there evidence for coding potential? 
Yes, there is evidence for coding potential. GeneMark S indicates intergenic coding potential. GeneMark displays indicative coding potential 
Atypical and typical ps on GeneMarkS 
GeneMark shows good coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando 88 (91 on phamerator) is conserved in 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 52023 has strength 8.38" 
Does the start site have an associated ribosome binding site with a high score? 
52023 produces an excellent, and the best scoring RBS.  
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? 
Yes, this start site is conserved in 28 other phages (28MA) 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Strong start site conservation. Conservation of start site evidences that this indeed the right start site.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1 
51457is 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 91, a helix-turn-helix DNA binding protein.  
PhagesDB BLASTp: e-value =0 
NCBI BLASTp: e-value =  0 
DNA Master BLASTp: 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? 
High score to helix-turn-helix protein. E-value = .12. Database PFAM.  
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? 
Helix-Turn-Helix DNA binding protein 