Gene 10
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Glutamine deamidase (See attached document)
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 5769 has strength 7.64" 
Is there evidence for coding potential? 
Yes, there is strong evidence as indicated by GeneMarkS - pictured below.  Genemark showscoding potential.  
Is the gene present in other annotated genomes? 
No - as indicated by phamerator. Lewando gene 10 (11) is not conserved in the AU6 subcluster. 
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? 
Both call at 5769 
"Original Glimmer call @bp 5769 has strength 7.64" 
Does the start site have an associated ribosome binding site with a high score? 
5769 has a solid score for both. This supports that this is the start site due to the presence of a strong translational promoter in corresponding mRNA.  The 5778bp start site also has a start site of note, but a concerningly high spacer distance.  
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? 
No – not conserved (no conserved start site). Starterator, interestingly, showed that there were no equivalent start sites for any of the possible start sites.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Not really – does not align very well to other proteins (best query alignment is 9-5 match with Sporto_8) 
BlastP PhagesDB: Q9:S5 
BlastP NCBI: Q9:S5 
BlastP DNA Master: Q9:S5 
5769 is the start site. The next start site 5788 has a start site that has a excessively distant spacer distance for the Shine Dalgarno sequence.  
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? 
Yes, Lewando_10 alligns signficantly to Sporto_8, an amidase, on all three of the used database. This allignemnt yielded a score of 1130 on DNAmaster and had an e-value of 0, indicating the support behind said matchup. Further investigation may be required as the amidase function is not on the approved functions list. Peptidases are approved functions, further investigation is required.  
PhagesDB BLAST: e-value = 1e-130 
NCBI BLAST:  e-value = 2e-162. Extremely high scoring match to the Sporto_8 amidase.. 
DNA Master BLAST:  e-value = 0. High scoring matches to an amidase, hypotehtical proteins, structural proteins, and acetyltransferases.  
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? 
Quality match 
Notable match to a Gln_amidase, corrobarating amidase function previously determined when looking at sequence homology. This match is high scoring with proability 98.47 and e-value of .0000082. Further investigation may be required - as aidases are not on the approved function list.  
Databse: NCBI conserved domains 
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
No, the gene order of this region is not conserved. Fthe flanking gens 10 and 12 are not higly conserved which makesthis gene harder to call, as there is no clear function of this region of the phage genome.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Glutamine deamidase