Gene 41
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 31009 has strength 11.28" 
Is there evidence for coding potential? 
Yes, it is indicated that there is indeed a gene at this spot. Coding potential indicated strongly by GeneMark and additionally by GeneMarkS.  
Atypical and typical ps on GeneMarkS 
GeneMark Shows excellent coding potential 
Is the gene present in other annotated genomes? 
Yes, Lewando_41 (44 on phamerator) in conserved in all of 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 31009 has strength 11.28" 
Does the start site have an associated ribosome binding site with a high score? 
The 31009 start site produces an acceptable RBS in terms of final score and Z-value (-3.876 and 2.4 respectively).   
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 31009 start site is conserved as indicated by Starterator.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
No conservation in other phage proteins 
BLASTp PhagesDB: n/a - Q1:S1 
BLASTp NCBI: n/a - Q1:S1 
BLASTp DNA Master: Q1:S1 
30552is indeed 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? 
Conservation in other phages. No functional assignment attributed in similar proteins.  
PhagesDB BLASTp: e-value = 2e-10 
NCBI BLASTp: e-value =  2e-5 
DNA Master BLASTp: e-value = 1.9e-5 
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 
Transmembrane segments noted in HHPred.  
SOSUI indicates the presence of a membrane protein: 
DeepTMHMM additionally indicates the presence of TM segments: 
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_40-48 is no conserved. This region additionally has very few assigned functions to the proteins in this region. Therefore it is not evident what is the function of this part of the Lewando genome.   
Is the proposed function found on the SEA-PHAGES approved function list? 
Membrane protein 