Gene 52
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-3bp overlap 
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 34682 has strength 6.97" 
Is there evidence for coding potential? 
Coding potentilal is apparent - and is obeserved throug both GeneMark programs. .  
and typical ps on GeneMarkS 
GeneMark shows very indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_50 (53 on phamerator) in conserved in all of 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? 
"Original Glimmer call @bp 34682 has strength 6.97" 
Does the start site have an associated ribosome binding site with a high score? 
36482 has a weak, but the one of the best possible Z and final scores, of 1.6 and -6.1 respectivly.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start site results in the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 34105 start site is the most conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins, as indicated through Q1:S1 allignments in other phages.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
34682 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? 
This protein is conserved in other phages, but these proteins do not have indicated function in DNA Master. Score of 136 and e-value of 1e-32. A zeina membrane is marked as a match on NCBI and on DNA Master, but not on DNA Master.  
PhagesDB BLASTp: e-value = 3E-20 
NCBI BLASTp: e-value = 1E-24 
DNA Master BLASTp: e-value = 1E-24 
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 
Match to a protein with no functional assignment, on NCBI conserved domains.   
Transmembrane segments are noted.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Gene order from Lewando_47-57 is somewhat conserved in AU6, although this region has no functional assignments in phamerator. For this reason, it is impossibile to attribute any sort of function to this region.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 