Gene 45
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 32740 has strength 7.15" 
Is there evidence for coding potential? 
Coding potential is apparent - as primarily indicated through GeneMarkS.  
Atypical and typical ps on GeneMarkS 
GeneMark shows no coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_45 (48 on phamerator) in 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? 
"Original Glimmer call @bp 32740 has strength 7.15" 
Does the start site have an associated ribosome binding site with a high score? 
The start site has an exceptional Z-value of 3.191 and a final score of -2.236. Upstream start sites have weak scores.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, this start site results in the third longest possible ORF. Longer ORFs would not result in excessive overlap.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 32740 start site is the most conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1 
32470 is 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? 
While this protein is conserved in other phages, there are no matches with functional assignment. Highest scoring match is to Uzumaki_42 which scored a 152 and has a  an e-value of 3.5e-11.  
PhagesDB BLASTp: e-value = 3e016 
NCBI BLASTp: e-value =  1e-12 
DNA Master BLASTp: e-value = 3.5e-11 
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? 
No quality match 
Transmembrane segments noted by HHPred, not observed by SOSUI.  
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 from Lewando_40-48 is not conserved. This region additionally has very few assigned functions to the proteins in this region. Therefore it is not evident what is the function of this part of the Lewando genome.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 