Gene 12
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-10 overlap 
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 7103 has strength 13.63" 
Is there evidence for coding potential? 
Yes, both softwares display coding potential.  
Is the gene present in other annotated genomes? 
Somewhat, parts of Lewando_12 (14) are conserved in GantcherGoblin and 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? 
Both call at 7103 
"Original Glimmer call @bp 7103 has strength 13.63" 
Does the start site have an associated ribosome binding site with a high score? 
7103 has the best score, in terms of Z value and final score. This indicates that 7103 may be the start site, due to a 7103 start site promoting efficient translation.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, the 7103 start site does not result in the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, this start site at 7103 is the most conserved start site out of the all of the available options.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, this start site is conserved I'm other phages, primarily by those in the AU6 subcluster.  
BlastP PhagesDB: Q2:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master:Q1:S1 
7103 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? 
Yes, Lewando_12 alligns with other phage proteins, specifically to other AU6 subcluster proteins. Overall, this is indicative of simialirty at the seqeucne level. To note, there is no function assigned in the conserved matches. The highest scoring match was to Zeina_9 in DNA Master, of 619.  
PhagesDB BLAST: e-value = 2e-85 
NCBI BLAST:  e-value = 0 
DNA Master BLAST:  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 to the four standard databases 
PHROGS present a high scoring matchup to a viral strctural protein, marcated as a head and packaing protein. Match had a high probability of  99.77 and an e-value of 1e-19.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
As with gene 11, the gene order of this region is not conserved. Downstream proteins in Lewando are uncharecterized and not conserved in the AU6 subluster. Lewando_13 (15) does not appear elsewhere in AU6, additionally Lewando_11 (9) is absent. Given this divergence, one can say that gene order is not conserved. From this, one cannot assign function to this region due to the lack of conserved syntenny in AU6.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical Protein 