Gene 26
Phage Name: 
26
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Hypothetical protein (weak evidence of chaperone using "controversial" PHROGS but no frameshift found)  
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 20205 has strength 6.44" 
Is there evidence for coding potential? 
Yes, there is strong evidence -through both GeneMark programs 
GeneMark S indicates coding potential throughout the most of the gene. Both second and gforuth order coding potential are quite strong.  
GeneMark shows coding potnetial, especially towars the start and end of the gene. Intragenic coding potential is limited in spots 
Is the gene present in other annotated genomes? 
Yes, Lewando_26 (29 on phamerator) in in alll AU6 phages.  
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 20205 has strength 6.44" 
Does the start site have an associated ribosome binding site with a high score? 
20205 is the best scoring start site. Z value = 2.372. Final score = -4.014.  
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 of20205 is the only conserved start site. This indeed evidences that this is the correct start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein (Lewando_26) contains Q1:S1 matches throughout the AU6 subcluster. These matches are additionall to AU6 phages, and overalll indicate that the start site is consevred.  
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_26 is homolgous to other AU6 proteins. Unfortunately though, the proteins it is homologus to do not have a functional assignemt The highest scoring macth on DNA Master is to UZUMAKI_24 with score of n289 and e value of 5.4e-31 
PhagesDB BLAST: e-value = 2e-27 
NCBI BLAST:  e-value = 5e-31 
DNA Master BLAST:  e-value =5.4e-31 
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 tail fiber chaperone. Proabbility of 99 and E-value of 4.6 e-8. 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 conserved from Lewando_24-31. Thewse regions additionally appear to encode structural prtoeins. This indicates that the protein of interest here has structural function. Particularily structure seems to be geared towards forming the phage tail. This supports the call of this gene as a tail fiber chaperone. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein