Gene 19
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 
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 14088 has strength 4.41" 
Is there evidence for coding potential? 
Yes, there is evidence for coding potential. 
GeneMarkS shows strong coding potential, both through the exhibition of typical and atypical codon ps bias.  
GeneMark indicates moderate coding potential. There ae some spikes indicating strong codon bias, but overall coding potential is not exceptional.  
Is the gene present in other annotated genomes? 
Yes- as indicated by phamerator. Lewando_19 (22) is conserved in the AU6 subcluster. Uzumaki, GantcherGoblin, as well as other phages display homology to this protein.  
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 14088 
"Original Glimmer call @bp 14088 has strength 4.41" 
Does the start site have an associated ribosome binding site with a high score? 
140888 is the highest scored start site, with a Z value of 3.287 and a final score -2.095. This indicates that this start site produces a strong translatiional start site, however this resultes in a shorter ORF than other start sites with acceptable (albeit not as good) scores, such as 13968. 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, this start site does not result in the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, intrestingly the 14088 start site is the most conserved, although it does provide the longest possible ORF. This conservation evidences that 14088 is indeed the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, BLASTp indicates that the start site is conserved, through a plethora of Q1:S1 allignemnts.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
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? 
Lewando_19 alligns well with other phage proteins, and these phage proteins have no functional assignemtn (hypothetical proteins). The highest score is the DNA Master match to GancherGoblin_16 with a score of 933 and an e-value of 0.  
PhagesDB BLAST: e-value = 2e-99 
NCBI BLAST:  e-value = 2e-126 
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 
No quality match on the standard databse 
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 somewhat conserved. Upstrem, a hypothetical protein, tail-terminator, minor tail protein are all conserved.  Downstream, a single minor protein is conserved in Gantcher goblin, but there is a divergent region following that. This region does appear to be structrual though.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical Protein 