Gene 39
Phage Name: 
39
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 30552 has strength 10.18" 
Is there evidence for coding potential? 
Yes, there is strong evidence - as indicated by both GeneMark and GeneMarkS 
GeneMarkS shows exceptional second and fourth order codon bias 
GeneMark Shows coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_39 (42 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 30552 has strength 10.18" 
Does the start site have an associated ribosome binding site with a high score? 
30552 is a high scoring start site, with a Z value of 3.1 and final score of -2.4 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
This start site results in the second longest possible ORF. There would be no excessive overlap with the previous start site.  
Is the start site conserved in other genomes as indicated by Starterator? 
30552 is the best and only conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
The 30552 start site is conserved in other proteins.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1  
30552 is indeed 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? 
Lewando_35 shows strong homology to other phage proteins. These porin unfortunately do not have functional assignment.  
PhagesDB BLAST: e-value = 1e033 
NCBI BLAST:  e-value = 8e-34 
DNA Master BLAST:  e-value = 1.8e-27 
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 
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_40-46 is quite divergent and has few functional annotations. No function, therefore can be ascribed to this region.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 