Gene 47
Note: The original Lewando 46 gene was called a reverse gene by glimmer, but evidence does not support said call.  
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 GeneMark call @bp 33001" 
No strength on gene call, very strange.  
Is there evidence for coding potential? 
Coding potential indicated by both programs.  
Atypical and typical ps on GeneMarkS 
GeneMark shows coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_47 (50 on phamerator) in conserved in all of AU6. 
Does the gene violate any of the major guiding principles? 
No, but there is a gap of note upstream of the called start site.  
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 GeneMark call @bp 33001" 
Does the start site have an associated ribosome binding site with a high score? 
This site has a good Z value and final score. The upstream start site additionally scores decently.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, this start site results in the second longest possible ORF. Longer ORFs would not result in excessive overlap.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 32740 start site is the most conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is not conserved in other phage proteins. However alternate start sites would not resolve that issue. Early part of Lewando 47 is divergent/  
BLASTp PhagesDB: Q5:S6 
BLASTp NCBI: Q5:S6 
BLASTp DNA Master: Q5:S6 
33001 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? 
This proteins aligns well to other phage proteins, but haphazardly, these proteins do not have any known function. Best match of the phages DB blast is to Argan_44 with score of 238.  
PhagesDB BLASTp: e-value = 1e-53 
NCBI BLASTp: e-value =  1e-63 
DNA Master BLASTp: e-value = 3.5e-11 
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 
Match to PF19791.2 (family of unknown function) with probability 100 and e-value of 1.9e-36.  
Database: 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? 
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? 
Hypothetical protein 