Gene 11
Phage Name: 
11
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
-10 overlap 
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) 
Original Glimmer call @bp 6850 has strength 0.93 ** not called by GeneMark 
Is there evidence for coding potential? 
Little coding potential on Genemark, or GenmarkS, although there appears to be an ORF. There is some second order coding potential on GeneMarkS. The call strength on glimmer is quite low.  
Region as seen on GeneMarkS 
Region as seen on GeneMark 
To note - there is second order coding potential for a reverse gene in the same region.  
Is the gene present in other annotated genomes? 
No - as indicated by phamerator. Lewando gene 11 (12) is not conserved in the AU6 subcluster. 
Does the gene violate any of the major guiding principles? 
Yes, this is a gene. Although there is little coding potential in the forward direction, the reverse gene is an orphan gene. The forward gene just may be a gene expressed in small amounced, which could be influenced by the codon bias used in production. 
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 6850 has strength 0.93 ** not called by GeneMark 
Genemark calls a reverse gene.  
Does the start site have an associated ribosome binding site with a high score? 
6850 has a decent Z and final score, but contains a slightly short spacer sequence. Overall this indicates that this sequence could recruit a ribosome at the 6850 start site. 
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 start site is conserved, albeit to a small degree. Sporto_9 has a homologous start site. 
Is the start site conserved in other phage genomes as indicated by BLASTp? 
Yes this start site is conserved in other proteins 
BlastP PhagesDB: Q1:S1 
BlastP NCBI: Q1:S1 
BlastP DNA Master: Q1:S1 
If Lewando_11 is indeed a gene, 6850 seems to be 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? 
Lewando_8 displays homology to other phage proteins, namely SPORTO_9. SPORTO_9 is from a phage outside of the AU6 subcluster, yet has multiple homologous proteins to Lewando. SPORTO_9 does not have function attacheed. Highest scoring match is from DNA Master and has score of 275 and E value 2.8e-29.  
PhagesDB BLAST: e-value = 1e-92 
NCBI BLAST:  e-value = 0 
DNA Master BLAST:  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? 
No quality match 
While there are some matches with probability above 80, these matches do not derive from viral proteins, so it unlikely that Lewando_11 holds similaior 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 s not highly conserved. There is some sembelenecre of sequence similairitt, but there appear to be additional insertions into the Lewando sequence. Further, genes like gene 15 are not conserved elsewhere in AU6, yet appear in Lewando. Therefore, gene order here can be said to be divergent.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Hypothetical protein 