Gene 50
Phage Name: 
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 34105 has strength 10.72" 
Is there evidence for coding potential? 
Coding potentilal is apparent - and is strongly suggested throug both GeneMark programs. .  
Atypical 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 34105 has strength 10.72" 
Does the start site have an associated ribosome binding site with a high score? 
Strong Z value and Final score, indicating an RBS with a high score.  
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 
34105 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 phage, but homologous proteins do not have an assigned function. The best scoring match on NCBi is to GantcherGoblin_47 with e value 4e-32 and max score 119. This protein has no assigned function.  
PhagesDB BLASTp: e-value = 6e-36 
NCBI BLASTp: e-value =  4e-32 
DNA Master BLASTp: e-value = 2.3e-15 
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? 
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 