Gene 31
Phage Name: 
31
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Tail Fiber Proteins 
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 27563 has strength 8.79" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly through GeneMarkS 
GeneMark S shows typical and atypical ps which indicates codon bias. This codon bias indicates a gene bias. 
GeneMark shows some coding potential. This is normal though, for called genes, so it is likely a gene here as well.  
Is the gene present in other annotated genomes? 
Yes, Lewando_31 (34 on phamerator) in conserved in AU6. 
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 27563 has strength 8.79" 
Does the start site have an associated ribosome binding site with a high score? 
Out of the two possible start sites, the 27563 start site is the only one with some potential of being a legitimate translational promoter. In fact, it would produce a strong site for ribosomal recruitment. The Z value for this gene is 3.287 and final score is -1.954.  
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 27563 indicates promising levels of conservation.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage genomes, given the plethora of Q1:S1 alignments 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_31 aligns with other phage proteins, however these proteins do not have any functional assignment. The highest scoring match was the 337 scored match with e value 5.3e-39 from the DNA Master BLASTp.   
PhagesDB BLAST: e-value = 4e-33 
NCBI BLAST:  e-value = 5e-39 
DNA Master BLAST:  e-value = 5.3e-39 
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 on the four standard databases  
PHROGs indicates that this protein is a tail fiber protein - a minor tail protein. Probability of 94.56 and e-value of .12 
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
The gene order is conserved from genes LEWANDO_24-34 in AU6. Given the previous call of the Tape Measure protein and minor tail protein, plus apparent minor and major tail proteins in other phages in the proximal area, this region is may be functionally important for tail assembly. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Tail Fiber Protein 