Gene 84
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-3bp overlap 
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 Glimmer only 
"Original Glimmer call @bp 50268 has strength 3.67 ** not called by GeneMark" 
Is there evidence for coding potential? 
Yes, there is evidence for coding potential. GeneMark S indicates some intergenic coding potential. GeneMark displays little strong coding potential 
Only atypical ps on GeneMarkS 
GeneMark shows miniscule coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando 84 (87 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 50268 has strength 3.67 ** not called by GeneMark" 
Does the start site have an associated ribosome binding site with a high score? 
This start site scores well.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, this start site is conserved in 3 other phages (3 MA) 
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 
50268 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 weak, and these matches do not align to proteins with functional assignments. Highest scoring match is to GantcherGoblin 78.  
PhagesDB BLASTp: e-value = 2e-5 
NCBI BLASTp: e-value =  3e-5 
DNA Master BLASTp: e-value = 3.5e-5 
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 on Hhpred 
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? 
Hypothetical Protein 