Gene 44
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
MazG-like nucleotide pyrophosphohydrolase  
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 32283 has strength 11.78" 
Is there evidence for coding potential? 
Both GeneMark and GeneMarkS indicate significant coding potential.  
Atypical and typical ps on GeneMarkS 
GeneMark Shows solid coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_44 (47 on phamerator) in conserved in Uzumaki.  
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 31516 has strength 6.69" 
Does the start site have an associated ribosome binding site with a high score? 
The 32283 has a start site with a decently high score.  
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? 
The 31516 start site is well conserved. This displays that the selected start sit is indeed the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1 
32283 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 protein is conserved in other phages, but the matches do not have any functional assignment.  
PhagesDB BLASTp: e-value = 8e-62 
NCBI BLASTp: e-value =  1e-159 
DNA Master BLASTp: 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? 
PHROGs indicates that this protein may be a MazG-like nucleotide pyrophosphohydrolase through the observation of multiple proteins with MazG domains and a protein with pyrophosphohydrolase domains and MazG domains. Top match has probability of 99.94 and e-value 8e-25 
PFAM indicates a nucleotide modification domain which further corroborates the function: 
MazG like proteins have been noted in other bacteriophages ( [link]. Che12 gp40 is another database that indicates that MaxG like proteins in bacteriophages can have a size of ~100 amino acids and contain a single MazG like domain yet remain functional.  
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? 
MazG-like nucleotide pyrophosphohydrolase  