Gene 18
Sunday, April 30, 2023
3:42 PM
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Major 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 13199 has strength 7.17" 
Is there evidence for coding potential? 
Yes, there is strong evidence as indicated by GeneMarkS - pictured below.  Genemark showscoding potential.  
GeneMarkS displays both typical and atypical codon bias, indicating codifng potential. 
GeneMark displays strong coding potential throughout the gene. Far stronger than normal for GeneMark.  
Is the gene present in other annotated genomes? 
Yes indicated by phamerator, Lewnado_18 (Lewando 21) has homologues in Uzumaki and GantcherGoblin. This indicates that this is indeed a gene as homolgoous coding protiens exist in other AU6 genomes.  
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 13199 
"Original Glimmer call @bp 13199 has strength 7.17" 
Does the start site have an associated ribosome binding site with a high score? 
13199 has a solid score for both. Objectivly, its Z and Final scores are not amazing, being at -2.326 and -4.163 respectivly. It does present as a start site that provides the strongest possible 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? 
Yes, the 13199 is the most conserved start site, as well as being the only conserved start site. This indicates that the 13199 start site is indeed the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Not really – Lewando_18 alligns quite well to other phage proteins and additioally has the same start site as other AU6 phage proteins such as GantcherGoblin_15.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
13199 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_16 displays significant allignment to other phage proteins, and these phages excitidly have assigned function. The most niotable of these matches is to GantcherGoblin_15 a major tail protein (NCBI score of 550 and e-value of 0). 
PhagesDB BLAST: e-value = 1e-157 
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 
High scoring match to  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Yes, gene order in this region is conserved throughout AU6. Lewando_18 (phamerator 21) is flanked by the same two upstream genes through AU6 (a hypothetical protein and the tail terminator). Additionally, a conserved gene is located downsteeam throughout AU6. These proteins are all involved in virion assembly, as evidenced by the similair proximal proteins.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Major tail protein 