Gene 20
Phage Name: 
20
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Minor tail 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 14675 has strength 5.48" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly throiugh GeneMarkS 
GeneMark S indicates coding potential throughout the most of the gene (both through the typical and atypical ps). There is a blip in coding potential around 16150, which could be of note.  
GeneMark shows limited coding potential past 15200, especially towards the end of the gene.  
Is the gene present in other annotated genomes? 
Yes, Lewando_20 (23 on phamerator) in conserved in Argan, Zeina and GantcherGoblin. 
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 14675 has strength 5.48" 
Does the start site have an associated ribosome binding site with a high score? 
14675 is the highest scoring start site, with a Z Vvalue of 3.191 and a Final Score of -2.684. This indicates that this site provides the best transalltional start site out of all possibile start site options, evidencing it is a likely 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 start site of 14675 is the most conserved start site, which is evidence that this is additioanlly the start soite for Lewando.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein alligs well to other phage protein, and with the provided 14675 start site, shares start sites with other phage proteins. This indicates that this  start site is the 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_20 shiws signifcant homolgy to other proteins, and to peorns with functionctional matches. Lewando_20 alligns to GantcherGoblin_17 with an e-value of 0 and a score of 1515 (DNA Master). This protein has the functioma; assignment of minor tail protein.  
PhagesDB BLAST: e-value = 0 
NCBI BLAST:  e-value = 0 
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? 
Quality match 
The best match is to a collar spike protein in myoviridae (probability of 98.57 abd e-value of 9.3e-6). The collar spike protein is a protein that is part of the myoviridae tail, located proximal to the capsid head.  
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 not quite conserved. Upstrem, a hypothetical protein, tail-terminator, major tail protein,and a second hypiothetical protein appear throughout the AU6 subcluster.  Downstream, though, there is a divergent region in the AU6 subcluster.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Minor tail protein 
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