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The following table (image linked below) shows promoter sequences recognized by different sigma factors. The sequence given for, e.g. sigma B is "GTTTaa"; why are the "a"s lowercase? Thanks!

![From "A sigma factor toolbox for orthogonal gene expression in Escherichia coli", Bervoets et. al. 2018]1

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    $\begingroup$ How would we know, without reading the paper, which you can do yourself? It is in no way a standard convention, as some databases have all nucleotides in lowercase. $\endgroup$ – David May 16 at 18:22
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    $\begingroup$ The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the most common nucleotide is given in lower case. That said, I'm not sure what the cut-off would be between "highly conserved" and "most common" and, in my opinion, is something that should be explained in the paper (though, in this case, it does not appear to be). There may be some convention I am unaware of. $\endgroup$ – canadianer May 16 at 19:25
  • $\begingroup$ @canadianer Can you make that an answer rather than a comment? $\endgroup$ – Bryan Krause May 16 at 19:32
  • $\begingroup$ @BryanKrause Okay, though I don't particularly like ending an answer with "I am unaware". $\endgroup$ – canadianer May 16 at 20:13
  • $\begingroup$ Here's a link to the paper, for those interested: ncbi.nlm.nih.gov/pmc/articles/PMC5829568 No mention of what the frequency cutoffs are for conserved-bases/less-conserved-but-higher-than-background-bases, but contacting the authors may help with getting specific percentages. (That's what the contact info is for!) $\endgroup$ – Alex Reynolds May 17 at 2:16
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The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the most common nucleotide is given in lower case. That said, I'm not sure what the cut-off would be between "highly conserved" and "most common" and, in my opinion, is something that should be explained in the paper (though, in this case, it does not appear to be). This paper, for example, uses uppercase where a base is conserved in four of the five sequenced promoters. There may be some convention I am unaware of.

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