Gene 17.5
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 
Tail Terminator 
Annotation Decision 1 (Is this a gene?): 
Gathering Evidence 
Explain Your Rationale 
Was the gene called by an auto-annotation program (Glimmer, GeneMark) 
Is there evidence for coding potential? 
Limited coding potential indicated by GeneMarkS, no coding potential indicated by GeneMark 
GeneMarkS indicates solely indicates second order coding potential (atypical ps) 
GeneMark shows no coding potential 
Is the gene present in other annotated genomes? 
Yes Lewando_1.75 (on phamerator 20) is conserved in GantcherGoblin, Argan Uzumaki. This indicates that this is indeed a gene, due to the presence of homologous AU6 genes 
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? 
No call notes, not called 
Does the start site have an associated ribosome binding site with a high score? 
The 12970 start site has a weak RBC, with a Z value of .509 and a final score of -8.879, which is quite bad. The best start site, in terms of produciing an RNA with a solid RBS, would be the 12883 start site. The 12883 start site has the best score with a Z value of 2.113 and a final score of -4.479 respectivly.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, the 12883 start site provides the longest ORF. 
Is the start site conserved in other genomes as indicated by Starterator? 
The 12883 start site is the most conserved start site, which indicates that it is indeed the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes, as there are 1:1 allignemnts with many other phage proteins, especially with those in the AU6 subcluster. This homology in start site is strong evidence that 12883 is the correct atart site.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
12883 is 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 tail terminator proteins. The best match is to Zeina_15, a tail terminator, which had an e-value of 1e-44 and a max score of 150. 
PHAGES DB Blast - e-value of 4e-36 
NCBI BLAST:  e-value = 1e-44 
DNA Master BLAST:  N/A 
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: 
6TE9_F is the match of interest, as it corrrobarates the BLASTp matches to tail terminator protieins. This match has a probability of 95.97 and an e-value of .38. This is strong evidence that Lewando_17.5 encodes a tail terminator protein  
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 conserved happens to be conserved AU6, as the Lewando_17.5 homologous in GantcherGoblin and Uzumaki ptoteins aresurrounded by the major capsid and protease fusion protein, and a hypothetical protein upstream along with the mahir tail protein, a hypothetical protein and the minor tail protein.. This indicates that this section of this genome is relevent for a tail assembly and overall capsid assembly.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Tail terminator 