Gene 63
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
DNA Primase/Polymerase/helicase 
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 38997 has strength 6.89; GeneMark calls start at 39087" 
Is there evidence for coding potential? 
Coding potential is apparent - as indicated by GeneMarkS. Good coding potential indicated by GeneMark. This is especiallly indicative given gene length 
Both typical and atypical ps on GeneMarkS 
GeneMark shows sufficent indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_63 (66 on phamerator) homologues are conserved in all of AU6n. 
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 38997 has strength 6.89; GeneMark calls start at 39087" 
Does the start site have an associated ribosome binding site with a high score? 
38997 has a food Z value and final score 
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Is the start site conserved in other genomes as indicated by Starterator? 
38977 is most conserved 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This start site is conserved in other phage proteins, as indicated through Q1:S1 alignments in other phages.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1 
34095 is the start site.  
Annotation Decision 3 (What is the function of the putative protein?): 
Gathering Evidence 
Explain Your Rationale 
Does this protein align with a protein having a functional assignment in BlastP (phagesDB and/or GenBank) with an alignment of 10-4 or smaller with appropriate coverage? 
DNA Master + Phages DB + NCBI: 
DNA primase/polymerase 
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? 
Is this gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
Yes - synteny is observed 
Phamerator 
This gene is in a Pham with over 150 other genes in the AU6 subcluster and other subclusters 
This suggests a conservation of this gene within the AU6 subcluster and in other subclusters as well 
It is worth noting that most of the members in this Pham have been labeled with a function "DNA primase/polymerase" 
The region in which this gene is located also has a high alignment with other phages in the AU6 subcluster 
This suggests not only is the gene conserved, but also the region in which the gene is located is conserved. 
Displayed many alignments with 0e0 e-valuesand 1:1 alignment scores 
This suggests high conservation of this gene across phages 
Supports the results from Phamerator 
It is worth noting that with the predicted conservation, most of the alignments gene have a proposed function of  "DNA primase or DNA polymerase" 
Supports the results from phamerator  
*Phage DB  & Phamerator Lewando gene 66 corresponds to Lewando gene 63 on DNA Master* 
Is the proposed function found on the SEA-PHAGES approved function list? 
Yes - DNA primase/polymerase/helicase protein is in the SEA-PHAGE approved function list 
There are no restriciton associated with this function other than ensuring all domains of this protein are found. 
DNA primase/polymerase/helicase - due to high alignments with proteins of DNA primase/polymerase functions in Blastp and Phamerator. Probability scores over 90% were seen for helicase, primase and polymerase proteins on HHPred. This supports calling the function DNA primase/polymerase/helicase since all three domains are found. 