Gene 32
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 28063 has strength 1.67" 
Is there evidence for coding potential? 
Yes, there is evidence - predominantly through GeneMarkS 
GeneMarkS shows strong typical ps upstream and throughout the gene. Strong evidence that there is indeed a gene here.  
GeneMark shows no coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_32 (35 on phamerator) in conserved in one other phage in AU6. 
Does the gene violate any of the major guiding principles? 
Yes, there is a large gap between Gene 31 and 32, with respect to the called start and stop sites. A BLASTx search revealed coding potential in this 'non-coding region' although this region could indeed be part of the gene.  
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 28063 has strength 1.67" 
Does the start site have an associated ribosome binding site with a high score? 
The 28063 start site has a comparatively poor score. The 27799 start site is of interest due to its ORF length an 'relatively' decent z value and final score. However, all of the start sites are  
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? 
Starterator doesn't indicate the presence of any equivalent start sites in other phages.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein given the 27799 start site would align Q1:S1 to other phage proteins. This indicates the 27799 start site is indeed the start site.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S89  
27799 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_35 aligns well to other phage proteins. Some of these proteins have assigned function of minor tail proteins. Qui_44 is a homologous phage protein with functional assignment of minor tail protein.  
PhagesDB BLAST: e-value = 1e-70 
NCBI BLAST:  e-value = 5e-81 
DNA Master BLAST:  e-value = 4.7e-22 
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 most informative match is to phrog_6977 which is a minor tail protein. Probability of 98.17 and e-value of .00083 
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? 
Minor tail protein 