Gene 71
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 44727 has strength 7.11" 
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? 
No. this gene is not conserved. 
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 44727 has strength 7.11" 
Does the start site have an associated ribosome binding site with a high score? 
No, this start site is mediocre scoring. It has the second highest final score, with the 44925 start site having a slightly higher score.  
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. Note: some Q4:S7 alignments appear as well.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q4:S71 
44727 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 Count_82. 
PhagesDB BLASTp: e-value = 2e-11 
NCBI BLASTp: e-value =  2e-9 
DNA Master BLASTp: e-value = 1.6e-9 
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 
Small parts of this protein align with proteins not on the SEA-PHAGES approved functions list.  
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_62-74 is conserved in AU6 and contains numerous DNA synthesis proteins, such as ssDNA binding proteins, DNA polymerase, and DNA helicase. For this reason, it is safe to assume that this region contains key DNA replication proteins for proliferation. This can be useful in function assignments.    
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical Protein 