Gene 36 
Phage Name: 
36
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 29377 has strength 7.45" 
Is there evidence for coding potential? 
Yes, there is strong evidence - throiugh both GeneMark and GeneMarkS 
Strong second and fourth order coding bias on GeneMarkS 
GeneMark Shows coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_36 (39 on phamerator) in conserved in all of the other current AU6 phages. 
Does the gene violate any of the major guiding principles? 
Not quite, but the upstream gap is of note. 
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? 
"Original Glimmer call @bp 29377 has strength 7.45" 
Does the start site have an associated ribosome binding site with a high score? 
29337 gas the best z value and final score, indicating that this start site could produce a translationally active RNA.  
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? 
29377 is well conserved, and is the only conserved, start site. 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein, given the 28935 start site, would be 1:1 with other phage protein. This indicates that this start site would indeed be the correct start site, as other phage share this same start site.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1  
28935 is indeed 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? 
Lewando_36 is homologous to other proteins, such as Zeina_34, but these proteins do not have functional assignment.  
PhagesDB BLAST: e-value = 7e-48 
NCBI BLAST:  e-value = 6e-70 
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? 
No quality match 
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
The gene order from genes LEWANDO_31-37 in AU6 is somewhat variable, and includes a list of hypothetical. Therefore it is hard to ascertain function from regional gene location. Downstream of this region is a divergent portion of the Lewando genome.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein