Gene 21
Phage Name: 
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 16467 has strength 7.48" 
Is there evidence for coding potential? 
Yes, there is evidence, derived primarily from GeneMarkS. GeneMarkS shows both atypical and typical ps, which inidcates that there is second and fourth order codon bias. GeneMark does not indicate a gene is present.  
Conding potential exhibited.  
Limited coding potential. 
Is the gene present in other annotated genomes? 
Yes, Lewando_21 (24 on phamerator) in somewhat conserved in Argan, Zeina and GantcherGoblin, as evidenced by green lined between Lewando_24 and GantcherGoblin and Uzumaki 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? 
"Original Glimmer call @bp 16467 has strength 7.48" 
Does the start site have an associated ribosome binding site with a high score? 
16467 is the only relevent start site at the 5' end of the gene, given its solid Z and final score of 2.389 and -3.899 respectivly. The other styart sites located towards the start of the ORF have quite weak ability to produce an ORF with a sufficent 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? 
The start site of 16467a conserved start site, and in fact the only conserved start site. This provides furthee backing that the 16467 start site is the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein has homologous start sites, as evidenced by BLASTp, given the oibserved the Q1:S1 allignemtns shown below.  
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_21 alligns to other phage proteins, namely Tokki_23 minor tail proteins, that have functional assignments. The score for the match on the PhagesDB blast received a 391 and an e-value of e-108.  
PhagesDB BLAST: e-value = 1e-108 
NCBI BLAST:  e-value = 1e-125 
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 top match was to 2FSD_A, a viral protein involved in the baseplate of a bacterial phage. This corroborates the fact that this protein is a tail protein, and likely a minor one as well. The baseplate protein functions on the official SEA-PHAGES function list do not maych up with the described protien. Probability of match = 97.75 and e-value = 8.7e-4.  
Database: PDBe 
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 largely conserved, and. Upstream Lewando_20, 19, 18, 17, and 16 are all conserved un the subcluster, outside of Uzumaki. Downstream, the next two genes are conserved. Given this, gene roder is conserved. All of these have fuunctions in assembly so Lewando_21 may function in phage capsid assembly as well.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Minor tail protein 