Gene 43
Phage Name: 
43
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-3bp Overlap 
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 31516 has strength 6.69" 
Is there evidence for coding potential? 
Yes, coding potential is apparent. GeneMarkS shows strong coding potential. GeneMark shows limited coding potential.  
Atypical and typical ps on GeneMarkS 
GeneMark Shows solid coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_43 (46 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 31516 has strength 6.69" 
Does the start site have an associated ribosome binding site with a high score? 
31516 provides a sufficient RBS. It has a z value of 1.977 and final score of -4.842.  
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 31516 start site is extraordinarily well conserved and indicates that the selected start sit is indeed the 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 
31516 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? 
Conservation in other phages. No proteins have functional assignment on the phagesDB blast. A Zeina protein has the functional assignment of membrane protein on DNA Master. This match scored a 1160 and had an e-value of 0.  
PhagesDB BLASTp: e-value = 8e-62 
NCBI BLASTp: e-value =  1e-159 
DNA Master BLASTp: 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? 
No quality match 
Transmembrane segments noted by HHPred 
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? 
Membrane protein 