"Shine-Dalgarno sequences are typically NOT found in the first gene of an operon but are mostly found in subsequent genes"

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Does anyone know how to find the SDp (Shine Dalgarno positive) and SDn (Shine Dalgarno negative) in a bacteria species?

(SDp and SDn)

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Michele L Williams

Take a read of:

Ma J, Campbell A, Karlin S. Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures. J Bacteriol 2002; 184: 5733-5745.

James C Hu

Incorrect. When there is a leaderless mRNA, the SD-independent translation is obviously for the first gene, but the opposite is not true.At least in Gram negative bacteria such as E. coli, leaderless mRNAs are relatively rare. Most operons have leaders with SD motifs for the first gene.