Gene 15
Phage Name: 
15
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 9648 has strength 8.46" 
Is there evidence for coding potential? 
Both genemark and genemarkS indicate coding potential. GeneMarkS shows both first and second order coding potential. GeneMark indicates coding potential to a lesser degree.  
Is the gene present in other annotated genomes? 
Yes - as indicated by phamerator. Lewando gene 15 (17) is conserved in the AU6 subcluster. Homogous are seen in GantcherGoblin, Uzumaki, and Zeina.  
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 5769 
"Original Glimmer call @bp 9648 has strength 8.46" 
Does the start site have an associated ribosome binding site with a high score? 
The 9648bp produces an mRNA a low scoring start site, with a Z value of 1.619 and final score of -5.724. This could present an example of co-transcriptional regulation, as other start sites encode significantly shorter RNAs.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes it 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? 
Yes, the 9648 start site is the most conserved start site. This indicates that this start site is indeed the correct start site - through the demonstration of species homology. 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, this start site is conserved in GantcherGoblin as indicated by BASTp NCBI and DNA Master. The PhagesDB BLAST match indicates a one bp slippage, but no alternate start site could correct this. Overall, this evidences the 9648 start stie, due to homology in other phage proteins.  
BlastP PhagesDB: Q4:S5 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
Gene starts at 9648 
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? 
Lewando_16 displays significant allignment to other phage proteins, however these proteins do not have assogned function. The highest scoring match is to GANTCHERGOBLIN_11, which scored a 760. Alternate means are required to elucidate function.  
PhagesDB BLAST: e-value = 1e-98 
NCBI BLAST:  e-value = 1e-111 
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? 
Quality match 
High scoring match to the another phage minorr head protein. 90.35 score and an E value of 59.  
Database: PHROGS 
Note, no quality matches were found in the four typical databases.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Yes, gene order in this region is conserved throughout AU6. Lewando_15 homologoues are flanked by portal and major capsid and protease fusion proteins in the AU6 genomes. Given this, it is reasonable to assume that this protein is involved in phage particle assembly.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein