Gene 35
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
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 28935 has strength 7.19" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both GeneMark and GeneMarkS 
Atypical and typical ps on GeneMarkS 
GeneMark Shows coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_35 (38 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 28935 has strength 7.19" 
Does the start site have an associated ribosome binding site with a high score? 
28935 has a fantastic Z value (3.189) and good final score (-2.335). 
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? 
28935 start site conserved in Starterator 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein, given the 28935 start site, would be 1:1 with other phage protein. This indicates that this start site would indeed be the correct start site, as other phage share this same start site.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1  
28935 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 proteins ten to be holing proteins. The DNA Master match has a score of 550, e-value of 0, and aligns to GantcherGoblin holing.  
PhagesDB BLAST: e-value = 2e-55 
NCBI BLAST:  e-value = 6e-70 
DNA Master BLAST:  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? 
Quality match 
The most informative match is to PF16938.8 and e value of 2/3e-26. This match is to a holin. Database is CDD.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
The gene order from genes LEWANDO_31-37 in AU6 is somewhat variable, and includes a lot of hypothetical. Therefore it is hard to ascertain function from regional gene location.  
Is the proposed function found on the SEA-PHAGES approved function list? 