Gene 30
Phage Name: 
Stop Coordinate 
Direction (Forward or Reverse) 
Gap (Overlap) with Previous Gene 
Selected Start Coordinate 
Selected Function 
Minor tail 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 26378 has strength 4.81" 
Is there evidence for coding potential? 
Yes, there is strong evidence - predominantly through GeneMarkS 
GeneMark S shows second order and fourth order codon bias throughout the length of the gene. There are some small blips, but no indication that this is not a gene.  
GeneMark shows limited coding and contains two small intragenic blips. Overall this makes it seem like a gene is here.  
Is the gene present in other annotated genomes? 
Yes, Lewando_30 (33 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 26378 has strength 4.818" 
Does the start site have an associated ribosome binding site with a high score? 
The 26478 has a god Z value of 2.478 and a solid final score of -3.713. Overall this indicates that is a start site that can produce in a translationally active RNA.  
Is the predicted start codon the longest ORF? If not, does the longest ORF result in excessive overlap (>30bp)? 
This start site results in the second longest possible ORF. There would be excessive overlap with the previous start site.  
Is the start site conserved in other genomes as indicated by Starterator? 
The 26378 start site of is the very conserved. In fact, it is the most and only conserved start site, which is evidence that this is additionally the start site for Lewando.  
Is the start site conserved in other phage genomes as indicated by BLASTp? 
This protein, given the 26378 start site, would be 1:1 with other phage protein. This indicates that this start site would indeed be the correct start site, as other phage use this same start site.  
BLASTp PhagesDB: Q1:S1 
BLASTp NCBI: Q1:S1 
BLASTp DNA Master: Q1:S1  
14675 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_30 aligns with a plethora of other phage proteins, and has high scoring matches to other AU6 proteins. The best match is to GantcherGoblin_33 which scored a 1652 on DNA Master BLASTp and had an e-value of 0. This protein, as well as other proteins similar to Lewando_30 have assignment of minor tail proteins.  
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 
The most informative match is to 3d37_A, a tail protein with probability of 99.61 and e value of 7.3e-12. Database is CDD.  
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 is conserved from genes LEWANDO_24-34 in AU6. Given the previous call of the Tape Measure protein and minor tail protein, plus apparent minor and major tail proteins in other phages in the proximal area, this region is may be functionally important for tail assembly. 
Is the proposed function found on the SEA-PHAGES approved function list? 
Minor tail protein 