Gene 38
Phage Name: 
38
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
30181 (30166 seems equally acceptable, coin toss)
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 30181 has strength 6.13" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both GeneMark and GeneMarkS 
Atypical and typical ps on GeneMarkS. This indicates that this region of the phage genome can be effectively translated.  
GeneMark Shows coding potential 
Is the gene present in other annotated genomes? 
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 30181 has strength 6.13" 
Does the start site have an associated ribosome binding site with a high score? 
The 30181 start site has the, comfortably, best SD with a Z value of 3.2 and final score of 2.2. To note, the upstream 30166 also has an acceptable SD score.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
The 30166 start site results in the longest possible ORF - evidencing that this is the start site through maximizing coding potential.  
Is the start site conserved in other genomes as indicated by Starterator? 
Orphan gene - no start site conservation.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein, given the 28935 start site, would be 1:1 with other phage protein. This indicates that this start site would indeed be the correct start site, as other phage share this same start site.  
BLASTp PhagesDB: Q4:S1172 
BLASTp NCBI: n/a 
BLASTp DNA Master: Q12:S421  
30166/30181 is indeed 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? 
No quality alignment to other phage proteins.  
PhagesDB BLAST: e-value = 9.4 
NCBI BLAST:  e-value = n/a 
DNA Master BLAST:  e-value = 2.78 
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_40-46 is quite divergent and has few functional annotations. No function, therefore can be ascribed to this region.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 