Gene 48
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 33356 has strength 9.66" 
Is there evidence for coding potential? 
Both sources indicate coding potential to a solid degree.  
Atypical and typical ps on GeneMarkS 
GeneMark shows no coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_48 (51 on phamerator) in conserved in all of AU6. 
Does the gene violate any of the major guiding principles? 
Not really, Lewando 48 is a short gene though, at 119 bp, so further investigation could be required.  
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 33356 has strength 9.66" 
Does the start site have an associated ribosome binding site with a high score? 
The start site has a sufficient Z value and final 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? 
No conservation in start sites.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is not conserved in other phages. The only observed alignments were 3:4 and 1:2 alignments. This indicates, given the lack of alternate start sites, that the start of Lewando_48 is divergent.  
BLASTp PhagesDB: Q3:S4 
BLASTp NCBI: Q3:S4 
BLASTp DNA Master: Q3:S4 
33356 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 somewhat conserved, although no function is attributed to closely related proteins.  
PhagesDB BLASTp: e-value = 3e-13 
NCBI BLASTp: e-value =  1e-14 
DNA Master BLASTp: e-value = 1.3e-14 
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_40-48 is not conserved. This region additionally has very few assigned functions to the proteins in this region. Therefore it is not evident what is the function of this part of the Lewando genome.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 