Gene 54
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 GeneMark call @bp 35003" 
Is there evidence for coding potential? 
Coding potentilal is apparent - and is strongly suggested throug both GeneMark programs. .  
Atypical and typical ps on GeneMarkS 
GeneMark shows very indicative coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_54 (57 on phamerator) in conserved in GantcherGoblin.  
Does the gene violate any of the major guiding principles? 
Yes, it is quite short, <120 bp.  
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 GeneMark call @bp 35003" 
Does the start site have an associated ribosome binding site with a high score? 
Strong Z value and Final score, indicating an RBS with a high score attributed to the 36003 start site.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
Yes, this start site results in the longest possible ORF.  
Is the start site conserved in other genomes as indicated by Starterator? 
No homologous start sites.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
No conservation in start site, start if Lewando_54 is divergent.  
BlastP PhagesDB: Q1:S4 
BlastP NCBI: Q1:S2 
BlastP DNA Master: n/a 
35003 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? 
This protein is conserved in other phage, but homologous proteins do not have an assigned function, as per the phagesDB BLASTp.  
PhagesDB BLASTp: e-value = 5e-9 
NCBI BLASTp: e-value =  1e-19 
DNA Master BLASTp: e-value = no match 
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 
Match to the DUF4236 family of proteins, but this family has no assigned function. Database, NCBI conserved domains.  
HHPRED incated TM segments.  
DeepTMHMM confirms TM segments. TM segment longer than 17 bp.  
SOSUI confirms TM segment 
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_47-57 is somewhat conserved in AU6, although this region has no functional assignments in phamerator. For this reason, it is impossibile to attribute any sort of function to this region.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Membrane protein 