SEA-PHAGES | integration cassette

integration cassette

Link to this post \| posted 13 Aug, 2018 18:03
welkin	The integration cassette– integrase, immunity repressor, and excise – are well-characterized in BPs, including function and confirmed start sites. See Broussard et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557535/#SD1

Link to this post \| posted 20 May, 2022 19:20
Pollenz	Many of the G1 phages are highly conserved at the nucleotide level in the region between the last reverse gene (immunity repressor) and first forward gene (cro). The operator site can be used to guide the annotation and is 5'-CGACATATGTCG-3'. Note that wet lab data supports the identification of the putative -10 and -35 binding sites and this orients the location of the CORRECT start codon (see the paper referenced above). In some cases, the DNA master RBS scores for the correct start site ARE NOT VERY GOOD and the start may not have been chosen by Genemark or Glimmer. However the wet lab data from BPs should be used to annotate the proper starts. Note that this results in smaller protein products, but DOES NOT reduce HHpred hits to the relevant PDBs or truncate N-terminal amino acid sequences. Remember that the intergenic region when moving from a reverse to forward gene MUST contain a sufficient gap (usually of at least 50bp) to accommodate these regulatory regions for transcription of these genes. RS Pollenz

Link to this post | posted 20 May, 2022 19:20

Pollenz

Many of the G1 phages are highly conserved at the nucleotide level in the region between the last reverse gene (immunity repressor) and first forward gene (cro). The operator site can be used to guide the annotation and is 5'-CGACATATGTCG-3'. Note that wet lab data supports the identification of the putative -10 and -35 binding sites and this orients the location of the CORRECT start codon (see the paper referenced above). In some cases, the DNA master RBS scores for the correct start site ARE NOT VERY GOOD and the start may not have been chosen by Genemark or Glimmer. However the wet lab data from BPs should be used to annotate the proper starts. Note that this results in smaller protein products, but DOES NOT reduce HHpred hits to the relevant PDBs or truncate N-terminal amino acid sequences. Remember that the intergenic region when moving from a reverse to forward gene MUST contain a sufficient gap (usually of at least 50bp) to accommodate these regulatory regions for transcription of these genes.

RS Pollenz

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integration cassette