Gene 27
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Hypothetical 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 20532 has strength 4.77; GeneMark calls start at 20595" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly throiugh GeneMarkS 
GeneMark S indicatestyoical ps and artypical ps throughout the region of Lewando_27. This indicates a gene is presdent.  
GeneMark shows limited coding potential. No coding potential at the start of ORF.   
Is the gene present in other annotated genomes? 
Yes, Lewando_27 (30on phamerator) is conserved in all of 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? 
Disagreement in calls. Glimmer calls at 20532 and 20595.  
"Original Glimmer call @bp 20532 has strength 4.77; GeneMark calls start at 20595" 
Does the start site have an associated ribosome binding site with a high score? 
20592 and 20595 are two proximal start sites, labelled 2 and 3 respectively. The 20595 has a better Z value and final score. The z value for the 20592 is 2.357 and the final score is -4.904. These are the best possible two here.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, but the 20592 start site results in the second longest possible ORF. The first start site would result in excessive overlap and would not be able to strongly bind a ribsome in translation.  
Is the start site conserved in other genomes as indicated by Starterator? 
The start site of 20532 is the only conserved start site. No conservation in the 20595 start site. This evidences that 20532 is the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein shares start sites with other phage proteins, as evidenced by the 1:1 BLASTp allignemnt. Uzumaki, Zeina, and Ghantcher Goblin proteins appear here 
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1SS1 
BlastP DNA Master: Q1:S1  
20532 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 alligns with other proteins, but these proteins by in large do not have functional assignment. Select proteins are assigned as minor proterinsd (such as synepsis_24 amd tokki minor tail protein). The match to syne[sos_24 has an e-value of 4e-50 and a score of 194.  
PhagesDB BLAST: e-value = 8e-65 
NCBI BLAST:  e-value = 7e-72 
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 minor capsid protein. The second best match is to a minor tail protein. The scoees are 99.41 and 99.13 respectivly. The e-values are 1.3e-112 and 5.6e-10 respectivly. Both matches come from CDD.  
Since the BLASTp matches somewhat indicate that this is a minor tail protein, this protein will be called as a minor tail protein.  
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