Gene 49
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 33491 has strength 14.42" 
Is there evidence for coding potential? 
Yes, strong evidence for coding potential 
Atypical and typical ps on GeneMarkS 
GeneMark shows strong coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_49 (52 on phamerator) in conserved in all of AU6 outside of Uzumaki. 
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 33491 has strength 14.42" 
Does the start site have an associated ribosome binding site with a high score? 
Yes, this site has a strong z value and final score.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start site results in the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 33491 start site is the most conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1 
33491is 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? 
While this protein is conserved in other phages, there are no matches with functional assignment. The highest scoring match in DNA Master is to Zeina-$8 with a score of 741 and an E-value of 0.  
PhagesDB BLASTp: e-value = 3e-77 
NCBI BLASTp: e-value =  2e-100 
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? 
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_47-57 is somewhat conserved in AU6, although this region has no functional assignments in phamerator. For this reason, it is impossible to attribute any sort of function to this region.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 