Gene 25
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Hypothetical protein (weak evidence of tail fiber using PHROGS)
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 19288 has strength 14.91" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both GeneMark and GeneMarkS 
GeneMark S indicates coding potential throughout the gene, of both second and fourht order. 
GeneMarkS displays coding potential for this gene call. To not GeneMark displays coding potential in other frames as well.  
Is the gene present in other annotated genomes? 
Yes, Lewando_25 (28 on phamerator) in conserved in Argan, Zeina and GantcherGoblin, as well as inother phages throughout 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 19288 has strength 14.91" 
Does the start site have an associated ribosome binding site with a high score? 
19288 has an excellent Z calue (3.287) and rinal score (-2.481). This evidences thisstart site as the cprrect one, especially since it yields a strong translational 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? 
The selected start site is the only conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein alligns 1:1 with many phage proteins. This indicates conservation in start site.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1  
14675 is 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? 
Lewando_25 is homologous to other phage rptiens, although these proteins do not have assighed function. The highest scoring match on PhagesDB BLASTp is to Tokki_21 which had an e-value of e-173 and score of 421. Tokki_20 does not have assigned fucntion 
PhagesDB BLAST: e-value = 1e-117 
NCBI BLAST:  e-value = 3e-60 
DNA Master BLAST:  e-value = 0 
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 on standard databases  
Quality match (es) on PHROGs. 3 high scoring matches were found, all of which were tail or tail fiber proteins. The highest scoring tail fihber protein match had a probability of 89.39 anmd E value of 51. 
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 is conserved from Lewando_24-31. Thewse regions additionally appear to encode structural prtoeins. This indicates that the protein of interest here has structural function. Particularily structure seems to be geared towards forming the phage tail.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein