Secondary structural model of sRk48/52 RNA candidates. (A) The model is based on sequence alignments performed with the genomic sequences in P. abyssi and extended to the four thermococcal genomes (P. horikoshii, P. furiosus, T. sibiricus and T. kodokarensis) (Additional file 6 Figure S5). (B) EMSA (upper panel) of the 5' end labeled 130 nt sRk52 RNAs in presence of L7Ae protein at 50, 100, 200 and 400 nM. The first lane (c) corresponds to the RNA without protein. The putative K-loop structure in the P2 stem is indicated (bottom panel).