Gene 72
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 45032 has strength 4.79" 
Is there evidence for coding potential? 
Yes, there is evidence for coding potential. GeneMark S indicates intergenic coding potential. GeneMark displays coding potential, but to a weaker extent 
Both typical and atypical ps on GeneMarkS 
GeneMark shows weak but sufficient indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, this protein is conserved in the entirety 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 45032 has strength 4.79" 
Does the start site have an associated ribosome binding site with a high score? 
Yes, 45032 is a high scoring start site 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start side leads to the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, this start site is conserved.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins, as indicated through Q1:S1 alignments in other phages.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q4:S71 
45032 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? 
This phage has high scoring matches to other phage proteins. These matches, though, are not to proteins with known function. Highest scoring match is to Argan_67 on DNA Master. 
PhagesDB BLASTp: e-value = 1e-57 
NCBI BLASTp: e-value =  2e-9 
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? 
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 loosly 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 