Gene 8
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Annotation Decision 1 (Is this a gene?): 
Gathering Evidence 
Explain Your Rationale 
Was the gene called by an auto-annotation program (Glimmer, GeneMark) 
Different calls – called by genemark at 3539 and glimmer at 3578. Overall though, both genes were called. 
"Original Glimmer call @bp 3539 has strength 10.55; GeneMark calls start at 3578" 
Is there evidence for coding potential? 
Yes – via genemarkS - as seen below.  Genemark also displays coding potential.  
Is the gene present in other annotated genomes? 
Gene 8 us conserved throughout the AU6 subcluster. GantcherGoblin (7), Uzumaki (8), Zeina (8) all contain a homologous gene to Lewando (9) gene 8.  
Does the gene violate any of the major guiding principles? 
No, this gene does not violate any of the 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? 
Called by genemark at 3539 and glimmer at 3578 
"Original Glimmer call @bp 3539 has strength 10.55; GeneMark calls start at 3578" 
Does the start site have an associated ribosome binding site with a high score? 
3539 has the highest score for both categories, suggesting that this start site is indeed the correct site. 3578 had a considerably worse Z and final score. Both fall in the acceptable range distance wise.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, the 3539 site provides the longest ORF - which supports this start site call.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, equivalent start sites are conserved in 121 other cases for the 3539 start site. This is strong evidence that this is indeed the start site. The 3578 start site is not conserved 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, conserved in Zeina_8. The alignment and full query cover between Lewando_8 and Zeina_8, as well as homology between the two genes, suggest that the correct start and stop sites were picked.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:1 
3539 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_8 is homologous to other phage proteins, specifically other terminase proteins. This is seen in all three of the search options, where Lewando_8 alligns to other terminase proteins in a high scoring fashion. Not all of these terminase proeins are in the AU6 subcluster. The highest scoring match is the PhagesDB Blast wherin allignment to Argan_7 was scored 1170 and had an E value of 0. 
PhagesDB BLAST: e-value = 1e-92 
NCBI BLAST:  e-value = 0 
DNA Master BLAST:  e-value = 0.0 
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? 
Quality match 
High scoring match to the another phage terminase protein. The score and E-value were significant, at 367.03 amd 4.5e-43 respcitvly. This iundicates high levels of homology between the two proteins. The highest scoring match was in PDBe.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
No, the gene order of this region is not highly conserved. Downstream proteins in Lewando are uncharecterized and not conserved in the AU6 subluster. Given this divergence, gene order is not conserved. Given such, it is difficult to assign a 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? 