Gene 16
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Major Capsid and Protease Fusion 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 10397 has strength 8.65" 
Is there evidence for coding potential? 
Yes, there is strong evidence as indicated by GeneMarkS - pictured below.  Genemark evidences coding potential.  
GeneMarkS displays sufficent coding potential, with strong first and second order coding potential in the region. 
GeneMark additionally shows coding potential throught the gene, outside of a blip around 10900bp. Strange that there is a loss in coding potnetial in this region. No dip is shown at this same spot in GeneMarkS 
Is the gene present in other annotated genomes? 
Yes, Lewando_16 (18 on phamerator) is conserved throughout AU6 
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 10397 
"Original Glimmer call @bp 10397 has strength 8.65" 
Does the start site have an associated ribosome binding site with a high score? 
The 10397bp start site has a oslid final score as well as Z value. These scores were 3.038 and -2.916 respectivly. Other downstream start sites have high scores, such as the 11129 start site, but they come at a loss of coding potential.  
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 10397 is conserved, and is in fact the only conserved start site out of 108 equivalent options. This indicates that this start site may indeed be the start site through 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Perfect conservation in start site across all three databases. This is another indicator that this start site is shared among other homolgous phage proteins.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
5769 is the start site. The next start site 5788 has a start site that has a excessively distant spacer distance for the Shine Dalgarno sequence.  
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. These proteins to which Lewando alligns to has functional assignemnt - to that of the major capsid and protease fusion protein. The DNA Master had a score of 2882 and an E-value of 0.  
PhagesDB BLAST: e-value = 0.0 
NCBI BLAST:  e-value = 0.0 
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? 
Quality match 
High scoring match to the another phage minorr head protein. 99.93 was the pprobability for that matchup with e alue of 6.2e-23  
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_16 homologoues are flanked by two hypothetical proteins. Additionally, it is fllanked at a secondary level by portal protein and tail terminator prootiens in other AU6 phages.    
Is the proposed function found on the SEA-PHAGES approved function list? 
Major Capsid and Protease Fusion Protein 