Gene 14
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) 
Called by both 
"Original Glimmer call @bp 8350 has strength 10.30; GeneMark calls start at 8371" 
Is there evidence for coding potential? 
Is the gene present in other annotated genomes? 
Yes- as indicated by phamerator. Lewando gene 14 (16) is conserved yhtoughoutthe AU6 subcluster. 
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? 
Different calls between the two databases - Glimmer calls at 8350 and GeneMark calls at 8371. GeneMarkS indicates weak coding potential near the start site, but strong coding potential downstream in the gene. GeneMark additionally indicates this weak coding potential at the start site, but stron intragenic coding potential. 
"Original Glimmer call @bp 8350 has strength 10.30; GeneMark calls start at 8371" 
Does the start site have an associated ribosome binding site with a high score? 
8350 has a higher Z-score and a better final score thean the 8371 start site. Frankly, the 8371 start site is one of poor strenth, and does not seem to be able to initiate translation effectively.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
The 8350 start site would result in the secodn longest ORF. The 8371 start site would result in an ORF that is 6 bp shorter.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 8350 start site is the most conserved start site, evidencing that it is indeed the correct start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, conserved in he Zeina_11 portal protein and with the Uzumaki portal protein. 1:1 subject query match.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
8350 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_14 alligns with multiple other AU6 homollgous proteins that have functional allignemnt. The DNA  Master allignemnet score to the Uzumaki portal protein is 1961, indicating significant homolohy.  
PhagesDB BLAST: e-value = 0 
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? 
Quality match 
High scoring match to the another phage portal protein. Score of 272.76, E value of 6.1e-33 and probability of 100. This overall indicates that this proteins contains the domains of a portal protein.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Like gene 13, the gene order around Lewando_14 is somewhat conserved. Downstream a homolohous hypothetical protein and the major capsid and protease protein appear. Downstream, it is a little messy, though, with lewando contianing different protiens than the rest of AU6. 
Is the proposed function found on the SEA-PHAGES approved function list? 