Gene 57
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 36086 has strength 6.50" 
Is there evidence for coding potential? 
Coding potential is apparent - from both algorithims.  
Both typical and atypical ps on GeneMarkS 
GeneMark shows indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_57 (60 on phamerator) homologues are conserved in all of AU6 outside of GantcherGoblin. 
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 36086 has strength 6.50" 
Does the start site have an associated ribosome binding site with a high score? 
36086 has a solid Z value and final score., in fact the best of all the start sites that produce ORFs of suitable length.  
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? 
36086 start site is 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 the protein align with a protein having functional assignment in BLASTp (phagesDB and/or GenBank) with an alignment of 10^-4 or smaller? 
No quality allignment. Best match on NCBI to GantchGoblin_51 with a sore of 127 and e value of 2e-39.  
PhagesDB BLASTp: e-value = 3e-45 
NCBI BLASTp: e-value =  4e-46 
DNA Master BLASTp: e-value = 1e-38 
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 the top 4 databases.  
Transmembrane segments noted. Deep TMHMM indicates: transmembrane protein 
SOSUI confirms 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? 
Gene order from Lewando_54-62 is predominantly conserved in AU6, although genes in this region have no functional assignments, for any other annotated phage, in phamerator. For this reason, it is impossible to attribute any sort of function to this region.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Membrane protein 