Gene 68
BASIC PHAGE INFORMATION 
Direction (forward or backwards) 
Gap (overlap) with previous gene 
1bp overlap
Selected start coordinate 
Hypothetical protein
Is this a Gene? 
Gathering Evidence 
Was the gene called by an auto-annotation program (Glimmer, GeneMark)? 
Is there evidence for coding potential? 
There is evidence of a strong coding potential around 43700-43850bp 
Is this gene present in other annotated genomes? 
Present in DNA Master auto-annotated genome and Pharmerator genome (called gene 71) 
Pharmerator: E-value = 0.000e+0 
Does the gene violate any major guiding principles? 
What is the Best Possible Start Site for this Gene? 
Gathering evidence 
What start site do Glimmer and GeneMark suggest? 
Glimmer @43708bp 
Gene Mark @43687bp 
Does the start site have an associated RBS with a high score? 
Start @43687bp: Z-score = 1.481; SD = -5.046; final score = -5.821 
Lower Z-score (<2) and final score  
ORF length = 162bp (longest) 
ATG start codon 
Start 43708@bp: Z-score = 1.703; SD = -4.580; final score = -5.626 
Better Z-score, but still low (<2) 
Slightly larger final score, but not by a huge margin  
ORF length = 141bp 
ATG start codon 
There is a start @43735bp that has better/larger Z-score and final score, however this would result in an ORF = 114bp, which violates the guiding principles. 
Likely not the start site  
Is the predicted start codon the longest ORF? If not, does it result in excessive overlap (>30bp)? 
Start @43687bp would give the longest potential ORF (162bp) with a 1bp overlap on the previous gene. 
Start @43708bp would give a slightly shorter ORF (141bp) and would not overlap on the previous gene. Instead there would be a gap of 21bp. 
Is this start site conserved in other phage genomes as indicated by Starterator? 
Start @43687bp (start #3): 
Found in 80% (4/5) genes in pham  
Called 75% of time when present  
Conserved in GantcherGoblin, Uzumaki, and Zeina phage  
Manually annotated 3 times for cluster AU6 
Start @43708 (start #4): 
Found in 40% (2/5) genes in pham  
Called 100% of time when present  
Conserved in Argan and Lewando phage  
Is this start site conserved in other phage genomes as indicated by BLASTp? 
There are only 4 BLASTp hits for this gene, all for AU6 phages  
Argan: E-value = 2e-13, q1:s1, 73% identity  
Uzumaki: E-value = 2e-05, q2:s9, 42% identity 
Zeina: E-value = 3e-05, q2:s9, 43% identity 
GantcherGoblin: E-value = 6e-05, q2:s9, 40% identity  
Start @43687bp 
What is the Function of the Putative Protein?  
Gathering evidence 
Explain rationale 
Does this protein align with a protein having a functional assignment in BLASTP (PhagesDB and/or GenBank) with alignment of 10-4 or smaller with appropriate coverage? 
Only 4 hits, all for function unknown  
No evidence of function  
Only none hit, for hypothetical protein 
E-value = 2e-07, q1:s1, 42% identity  
No evidence of function 
Does this protein align with a protein having a functional assignment in the PDB or other databases in HHpred with a probability of 90% or greater with appropriate coverage?  
There are no functions with >90% probability  
All functions have <55% probability  
53% probability for Brassinosteroid receptor island domain, E-value = 17, good coverage of gene  
50.5% probability for CARBOXYLESTERASE, E-value = 18, good coverage of gene  
Is this gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Deep TMHMM: 
No. of predicted TMRs = 0 
Pharmerator: 
Gene length and synteny are conserved in all AU6 phages  
There is no associated function with this gene  
No evidence of function  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein