Annotation notes and comments on phage Mitkao:

I. Positional annotation issues:
gene 62 54481-54537 is very short (i.e. smaller than general rule of minimum 30 a.a.), but identical gene has been annotated in SDcharge11, Phipps, and Kingveveve.


II. Functional annotation issues:
gene 67 56792-57094 hhpred analysis shows a 97.1% probability (e = .0026) of having a "ribbon - helix - helix" DNA binding domain. This term has not been used before for annotation of SEA phages. It appears to be the name of a superfamilty of DNA binding transcription factors. See Nature Reviews Microbiology 5, 710-720 (September 2007) | doi:10.1038/nrmicro1717
This function was added to the note in the minimalistic DNA master file and should therefore be removed if deemed by the annotation team to be inappropriate.

gene 59728-60333 hhpred analysis shows a 96.5% probably (e= 0.0051) hit to RNA polymerase sigma-H factor. This has not been annotated before by SEA phages. Function was added to minimalistic DNA Master file and should therefore be removed if deemed by the annotation team to be inappropriate.


III. tRNA comments
tRNA-scan and Aragorn detected NO tRNA features


IV. Other 

There are two gaps larger than 150 bp carefully examined:

1. region between genes 65 and 66; 454 bp gap, gap is between divergent genes, no significant blast hits, no significant coding potential, no glimmer/GeneMark gene predictions

2. region between gene 96 and 97; 162 bp gap, no significant blast hits, no coding potential, no gene predictions