Gene 29
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 25614 has strength 4.10; GeneMark calls start at 25545" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both algorithms 
GeneMark S indicates coding potential through hit entirety of this genes (both through the typical and atypical ps). Both typical and atypical ps have high magnitudes.  
GeneMark shows strong coding potential.  
Is the gene present in other annotated genomes? 
Yes, Lewando_29 (32 on phamerator) in conserved in all of the previously characterized AU6 genomes.  
Does the gene violate any of the major guiding principles? 
No. The upstream gap of 59bp is of slight note.  
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 25614 has strength 4.10; GeneMark calls start at 25545" 
Does the start site have an associated ribosome binding site with a high score? 
The 25545 start site is the higher scored start side. The 25545 start site has a z value of 2.546 and has a final score of -4.161. The alternate, glimmer called, 25614 start site has a has a Z value of 1.839 and a final score of -5.312. 25545 appears to be the better 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 25545 start site has a ton of conservation, 98 MA. The 25614 start site shows no conservation. This indicates that 25545 is the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Note, 25614 is the start site used in these BLASTp searches. 25545 appears to be the more apparent start site. The 25614 start site would produce an ORF that is 69bp shorter, 23 codons shorter, than the 25545 are site. For this reason a Q1:S24 match is expected. This was observed.  
BLASTp PhagesDB: Q1:S24 
BLASTp NCBI: Q1:S24 
BLASTp DNA Master: Q1:S24  
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_20 has amino acid level homology with other proteins as indicated by BLASTp. It is homologous to minor tail proteins. The best match is t Zeina)27, scoring 1014 with an e-value of 0 on the DNA Master BLAST.   
PhagesDB BLAST: e-value = e-146 
NCBI BLAST:  e-value = 2e-146 
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 to a collar spike protein in myoviridae (probability of 98.57 and e-value of 9.3e-6). The collar spike protein is a protein that is part of the myoviridae tail, located proximal to the capsid head.  
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 genes LEWANDO_24-34 in AU6. Given the previous call of the Tape Measure protein, plus apparent minor and major tail proteins in other phages, this region is likely integral for tail assembly. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Minor tail protein 