Gene 24
Phage Name: 
24
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 18478 has strength 10.33" 
Is there evidence for coding potential? 
Yes, there is strong evidence - as evidenced by GeneMarkS and GeneMark 
GeneMark S indicates coding potential through most of the gene, in both typical and atypical ps.  
GeneMark shows limited coding potential throughout the gene, with some spikes and some absent spots 
Is the gene present in other annotated genomes? 
Yes, Lewando_24 (27 on phamerator) in conserved in every other phage in the AU6 subcluster. 
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 18478 has strength 10.33" 
Does the start site have an associated ribosome binding site with a high score? 
18478 has the best Z Value and Final score, of 3.287 and -2.034 respectivly. This is indicative of this site producing a translationally active RNA transcript.    
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 18478 exhibits robust homology to the rest of the AU6 subluster. Overall, this conservation supports that 18478 is indeed the correct start site.   
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein has a start site that is conserved in other phages, as indicated by BLASTp.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1  
18478 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_24 is quite similair to other phage proteins. These proteins have functional assignment, almost unanimously as major tail proteins. The highest scoringh match was on DNA Master to the GantcherGoblin major tail protein. This match had a scire of 1215 and an e-value of 0.  
PhagesDB BLAST: e-value = 1e-144 
NCBI BLAST:  e-value = 1e-176 
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 toa tail tube protien (PF04630.15). This match had a probabiliity of 99.92 and e value of 6e-23. This corroborates that Lewando_24 is a astructutral protein and likely one that is a major tail protein. Databse: CDD. 
For this to be called a tail tube protein, phage must have a contractile tail 
Lewando is part of the Siphroviridae (non-contractile tail) 
Can't be a tail tube protein  
Research has shown (at least in lambda phage), the structure of the major tail protein in non-contractile phages is similar to the tail tube protein in contractile phages.  
Joshua M. Hardy, Rhys A. Dunstan, Trevor Lithgow, Fasséli Coulibaly, Tall tails: cryo-electron microscopy of phage tail DNA ejection conduits,Biochemical Society Transactions,50,1,(459-22W),(2022 
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.  
Is the proposed function found on the SEA-PHAGES approved function list? 