Gene 28
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
20912
Selected Function 
Tape Measure 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 20891 has strength 7.08" 
Is there evidence for coding potential? 
Yes, coding potital is displayed by both algotrithims 
GeneMarkS indicates coding potential throughout Lewando_28 
GeneMark displays coding potental intragenically. Coding potential is weak at the start of the gene.  
Is the gene present in other annotated genomes? 
Lewando_28 (31 on phamerator) homologues exist throughout AU6.  
Does the gene violate any of the major guiding principles? 
Not really, there is a pretty large gap between Gene 27 and 28 though. Could be of note.  
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 20891 has strength 7.08" 
Does the start site have an associated ribosome binding site with a high score? 
The 20891 has a low Z value, and poor final score (of 1.309 and -6.629 respectivly). Overall, other evidence would have to conserve the 20891 start site. The 20891 start site also has a short space distance. The 20912 start site is better.  
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. The 20912 start site that encodes a 21 base shorter ORF 
Is the start site conserved in other genomes as indicated by Starterator? 
The 20891 start site is not conserved in other genomes. Rather, the 20912 start site indicates has some conservation.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
All of the start sites here, via BLASTp, allign Q8 to S1, indicatig that the 20891 start site induces a 21 BP or 7 AA longer ORF/protein. Intrestingly, selecting the 21bp downstream 20912 start site would absolve this mis-allignment. This indicates that this 20912 start site is the start site through conservation in other phages.  
BlastP PhagesDB: Q8:S1 
BlastP NCBI: Q8:S1 
BlastP DNA Master: Q8:S1 
20912 is 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? 
Lewando_28 alligns to proteins with functional assignemtn. This function is unanimously as a tape measure protein. Strong similairty yo AU6 tape measure proteins. The DNA Master attributed an e calue of 0 and scor eof 5100 to the macth tiwth the Uzumaki tape measure protein.  
PhagesDB BLAST: e-value = 0 
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? 
Quality match 
High scoring  match, p=99.92 e-value=3.4e-14. Match again indicates this protein is a TMP. In conjunction with the BLASTp results, it seems that this protein is a TMP. Database - PDBe 
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 is conserved from genes LEWANDO_24-34 in AU6. Given this call of the Tape Measure protein, plus appparent minor and major tail proteins in other phages, this region is loikely integral for tail assembly. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Tape Measure Protein 