Gene 23
Phage Name: 
23
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 Glimmer call @bp 18312 has strength 9.98" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly throiugh both GeneMark GeneMarkS 
GeneMark S includes coding potential, and codoin bias of second and fourth order. 
GeneMark shows coding potential.  
Is the gene present in other annotated genomes? 
Yes, Lewando_23 (26 on phamerator) is conserved throughout 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 17438 has strength 7.79" 
Does the start site have an associated ribosome binding site with a high score? 
18312 provides the start site with the highes genomic Z value, of 3.298, and best final score of -1.931. This start site, however does not pprovide he longes t possible ORF, and signficiantly so. Fursther investigation is required.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
No, the 18312 start site results in a short ORF, and as such further analysis is required.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 18312 start site is the most conserved start site, which eviences that it is indeed the start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Perfect allignemtn and start site homology given the 18312 start site. Strong evidence that the 18312 start site is indeed the start site.  
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1  
18312 is the start site - as evidenced by this sites conservation in other phages.  
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_22 exhibits strong homology to a set of short phage proteinsd, although these proteins have no functional assignment. The highest scoring match is to Zeina_21 which had a score of 227 and e-value of 3.1e-23 on the DNA Master BLASTp 
PhagesDB BLAST: e-value = 3e-20 
NCBI BLAST:  e-value = 3e-23 
DNA Master BLAST:  e-value = 3.1e-23 
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 on standard databases 
PHROGs nly contained a match to a protei of unknown function 
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 is conserved both downstream and upstream of Lewando_23 (25 on phamerator). This region appears to encode many structuraal proteins, specifically in the phage tail.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 