Gene 40
Phage Name: 
40
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 30552 has strength 10.18" 
Is there evidence for coding potential? 
Yes, limited evidence. Atypical and typical ps indicates that this is indeed a gene on GeneMarkS.  
Atypical and typical ps on GeneMarkS 
GeneMark Shows no coding potential 
Is the gene present in other annotated genomes? 
No, Lewando_35 (38 on phamerator) is not 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 30552 has strength 10.18" 
Does the start site have an associated ribosome binding site with a high score? 
30844 is a high scoring site, as well as the only noted start site.  
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? 
Orphan gene, no Starterator.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
No conservation in other phage proteins 
BLASTp PhagesDB: n/a - no match  
BLASTp NCBI: n/a - no match 
BLASTp DNA Master: Q81:S208  
30552is 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? 
No notable conservation in other phage proteins 
BLASTp PhagesDB: n/a - no match  
BLASTp NCBI: n/a - no match 
BLASTp DNA Master: Q81:S208  
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_40-46 is quite divergent and has few functional annotations. No function, therefore can be ascribed to this region.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 