Gene 9
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 glimmer and genemark 
"Original Glimmer call @bp 5419 has strength 12.73" 
Is there evidence for coding potential? 
Yes, there is evidence in GeneMarkS as pictured below.  Genemark also indicated coding potential.  
Is the gene present in other annotated genomes? 
No, gene 9 (10) is not conserved in the AU6 subcluster as indicated by phamerator 
Does the gene violate any of the major guiding principles? 
No, although there is a solid gap between gene 8 and 9. This could be worthy of examination, but otherwise this does appear to be an independent gene.  
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 called at 5419 
"Original Glimmer call @bp 5419 has strength 12.73" 
Does the start site have an associated ribosome binding site with a high score? 
5419 has the best score overall - for final and Z scores - indicating that 5419 is indeed the start site. 
 5425 also has a high Z score, but a worse final score.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start codon would provide the longest ORF - supporting that this is the start site through  maximizing coding potential.  
Is the start site conserved in other genomes as indicated by Starterator? 
No, the 5425 start site is far more conserved (8 MA for 5425 vs 0 MA for 5419) 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
No, (9-6 alignment with Sporto_10). There was no real homology between Lewando_9 and other AU6 subcluster genes. 
BlastP PhagesDB: Q9:S6 
BlastP NCBI: Q9:S6 
BlastP DNA Master: Q6:S3 
5419 - provides the longest ORF. Additionally, the 5419 gene provides a gene with a better RBS.  
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 = 2e-61 
NCBI BLAST:  e-value = 0 
DNA Master BLAST:  e-value = 1e-11 
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 
HHPred suggested the presecnce of transmmebrane regions, however DeepTMHMM did not detect transmembrane regions 
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 conserved, atside of upstream terminase protein. No conclusions about functions on a regional basis could be ascertained.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 