Gene 22
Phage Name: 
22
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 17438 has strength 7.79" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly throiugh GeneMarkS 
GeneMark S includes coding potential, through codfon bias throughout the most of Lewando_22. Interestingly, therre is a blip in the middle of the gene, with no such bias. This region could be of interest for futurre study.  
GeneMark showsalmost no coding potential, outside of a small spile at 17500.  
Is the gene present in other annotated genomes? 
Yes, Lewando_22 (25on phamerator) is conserved throughout 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 17438 has strength 7.79" 
Does the start site have an associated ribosome binding site with a high score? 
17438  provides the optimal Z value and final score, of 3.289 and -1.993. No other start site wouldn provide an translatiojnal start siter with similair strenth. This evidences the start site as this particular start sit would provide an easlily translatable RNA transcipt.  
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 17438 is the most conserved start site. This further suggests the 17438 start site by examplifying that oither phages use this same start site (or are though to use this start site). 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
While the Lewando_22 protein is divergent from other AU6 proteins, its start site does not appeasr to be, Its start site is conserved, as evidenced through conservation in BLASTp in Uzumaki and Zeina.  
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_20 displayus significant similairit to Uzumaki_19, a minor tail ortien. This match had an e-value of 0 and score of 614 on DNA Master.  
PhagesDB BLAST: e-value = 3e-65 
NCBI BLAST:  e-value = 3e-74 
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 a baseplate protein in a Lactococcus Lactis phage. Intrestingly this match is to the same L. lactis protein matched up with in Lewando_21. The probability for thius match is 97.1 and e-vlaue is .032. This supports the match being a minor tail protien, as 2FSD_A appears to be a minor tail protein. 
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 both downstream and upstream of Lewando_22 (25 on phamerator). The predominat role pf tjese proteins a[[ears tp ne structural.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Minor tail protein 