Gene 37
Phage Name: 
37
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 29854 has strength 6.84; GeneMark calls start at 29839" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both GeneMark and GeneMarkS 
Atypical and typical ps on GeneMarkS 
GeneMark Shows coding potential 
Is the gene present in other annotated genomes? 
No, Lewando 37 (40) appears to be an orphan gene.  
Does the gene violate any of the major guiding principles? 
No, the upstream gap is of note, and could potentially be part of the gene.  
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? 
29854 (glimmer) and 29839 (genemark) 
"Original Glimmer call @bp 29854 has strength 6.84; GeneMark calls start at 29839" 
Does the start site have an associated ribosome binding site with a high score? 
29839 is the worse scoring start site, but encodes a longer ORF. 29854 is the better scoring start site but it encodes a shorter ORF.  
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 data 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
BLASTp does not provide data supporting any start site, given the divergence of Lewando_37 
BLASTp PhagesDB: Q4:S70 
BLASTp NCBI: n/a 
BLASTp DNA Master: n/a 
No matches 
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_37 shows limited homology to other phage proteins.  
PhagesDB BLAST: e-value = 3.2 
NCBI BLAST:  e-value = n/a 
DNA Master BLAST:  e-value = n/a 
No matches 
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 