Gene 34
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Membrane 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 28662 has strength 5.24" 
Is there evidence for coding potential? 
Yes, there is strong evidence - through both GeneMark and GeneMarkS 
GeneMark S shows second order and fourth order codon bias in the most of the game. There is a blip of note though around 28750.  
GeneMark indicates that there is coding potential in this gene, most of the coding potential seems to be concentrated towards the start of the gene.  
Is the gene present in other annotated genomes? 
Yes, Lewando_34 (37 on phamerator) in conserved in 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 28662 has strength 5.24" 
Does the start site have an associated ribosome binding site with a high score? 
28662 has a good scoring start site (with a z score of 3.083 and final score of -2.477). These are the best possible for this gene.  
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 28662 is the most and only conserved start site.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein's start site is conserved, as evidenced by Q1:S1 alignments.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1  
28662 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? 
Lewando_30 aligns with many phage proteins. Only one was observed to have a functional assignment, which was the match to Zeina Membrane Protein on DNA Master. This match had a score of 431 and e-value of 0.  
PhagesDB BLAST: e-value = 3e-50  
NCBI BLAST:  e-value = 3e-61 
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 - proteins were not possible phage proteins (lots of homology to HIV VpU) 
Transmembrane segment were detected.  
DeepTMHMM and SOSUI detected transmembrane domains - which suggests this is a membrane protein.  
Is the gene located adjacent to genes of known function and in a region of the genome that shows high conservation of gene order? 
The gene order from genes LEWANDO_31-37 in AU6 is somewhat variable, and includes a lot of hypothetical. Therefore it is hard to ascertain function from regional gene location.  
Is the proposed function found on the SEA-PHAGES approved function list? 
Membrane Protein 