Gene 42
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Membrane 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 31376 has strength 4.19" 
Is there evidence for coding potential? 
Yes, there is some coding potential. GeneMarkS is the primary indicator of coding potential as GeneMark only shows a small blip in support of that call site.  
Atypical and typical ps on GeneMarkS 
GeneMark Shows Noncoding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_42 (45 on phamerator) in conserved in all of AU6. 
Does the gene violate any of the major guiding principles? 
Not really, the gap between gene 42 is of note though. It is quite large and may contain its own gene.  
BLASTx indicated that there is no homologous gene to the gap between Lewando_41 and 42 
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 31376 has strength 4.19" 
Does the start site have an associated ribosome binding site with a high score? 
The 31009 start site produces an adequate RBS in terms of final score and Z-value (-2.939 and 2.856 respectively).   
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? 
Yes, the 31376 start site is shared in other phages as indicated by Starterator.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
BLASTp, overall, does not indicate full start site conservation. There is conservation early in the gene, but the first few residues are divergent.  
BLASTp PhagesDB: n/a - Q2:S3  
BLASTp NCBI: n/a - Q2:S3  
BLASTp DNA Master: Q2:S3  
31376 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? 
Conservation in other phages. The only other protein with functional assignment is to a Zeina membrane protein. This match has an e-value of 1.8e-12 and score 157. 
PhagesDB BLASTp: e-value = 6e-16 
NCBI BLASTp: e-value =  1e-17 
DNA Master BLASTp: e-value = 5e-13 
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 
Transmembrane segments noted 
SOSUI indicates the presence of a membrane protein: 
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_40-48 is not conserved. This region additionally has very few assigned functions to the proteins in this region. Therefore it is not evident what is the function of this part of the Lewando genome.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Membrane protein 