Gene 89
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 54752 has strength 4.12" 
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 some coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando 89 (92 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 54752 has strength 4.12" 
Does the start site have an associated ribosome binding site with a high score? 
This start site has a weak RBS. It is the strongest possible.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start side does lead to the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, this start site is conserved in 50 other phages (50 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 
54752 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 Uzumaki_71.  
PhagesDB BLASTp: e-value = 8e-34 
NCBI BLASTp: e-value =  3e-41 
DNA Master BLASTp: e-value = 3.2e-41 
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? 
Gene order from Lewando_70-80 is loosely conserved in AU6. This region, like the previously mentioned region contains many rep proteins involved in DNA replication. This regional function can be useful in function assignments.    
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical Protein 