Gene 66
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 43152 has strength 7.91" 
Is there evidence for coding potential? 
Coding potential is apparent - as indicated by GeneMarkS. Weak coding potential indicated by GeneMark. Indicative of the prescence of a gene.  
Both typical and atypical ps on GeneMarkS 
GeneMark shows sufficent indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_66 (69 on phamerator) homologues are conserved in all of AU6 outside of Argan. 
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 43152 has strength 7.91" 
Does the start site have an associated ribosome binding site with a high score? 
The start site has the best possible scoring start site, and it is a good scoring start site.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start side leads to the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
Yes, this start site is conserved.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins, as indicated through Q1:S1 alignments in other phages.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
DNA Master: 
34095 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? 
No quality alignment, as this phage protein does not align to other phage proteins with known function. There are high scoring matches, such as the match to Zeina_64.  
PhagesDB BLASTp: e-value = 23-28 
NCBI BLASTp: e-value =  5e-19 
DNA Master BLASTp: e-value = 4.7e-19 
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 on the top 4 databases.  
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_62-74 is conserved in AU6 and contains numerous DNA synthesis proteins, such as ssDNA binding proteins, DNA polymerase, and DNA helicase. For this reason, it is safe to assume that this region contains key DNA replication proteins for proliferation. This can be useful in function assignments.    
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 