Gene 60
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 37549 has strength 9.21; GeneMark calls start at 37444" 
Is there evidence for coding potential? 
Coding potential is apparent - as indicated by GeneMarkS. Good coding potential indicated by GeneMark.  
Both typical and atypical ps on GeneMarkS 
GeneMark shows sufficent indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_60 (63 on phamerator) homologues are conserved in all of AU6 outside of GantcherGoblin. 
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 37549 has strength 9.21; GeneMark calls start at 37444" 
Does the start site have an associated ribosome binding site with a high score? 
Weak SD and final score. 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Is the start site conserved in other genomes as indicated by Starterator? 
36549 is conserved in other phage genomes.  
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 
BLASTp DNA Master: Q1:S1 
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 allignment, as this phage protein does not allign to other phage proteins with known function. Best match on NCBI to Zeina_58 
PhagesDB BLASTp: e-value = 2e-13 
NCBI BLASTp: e-value =  2e-15 
DNA Master BLASTp: e-value = 1.4e-12 
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_54-62 is predominatly conserved in AU6, although genes in this region haveno functional assignments, for any other annotated phage, in phamerator. For this reason, it is impossible to attribute any sort of function to this region.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 