SSU rRNA secondary structure.

<p>The <i>P. falciparum</i> mt SSU rRNA secondary structure model is superimposed onto the <i>E. coli</i> SSU rRNA secondary structure model diagram. Regions where <i>P. falciparum</i> has no structure equivalent to <i>E. coli</i> are shown using gray circles and lines. Colored nucleotides compare the <i>P. falciparum</i> sequence to the Three Phylogenetic Domains/Two Organelles (aka 3P2O) consensus sequence from the Gutell lab’s Comparative RNA Web (CRW) Site [URL for CRW Site: <a href="http://www.rna.ccbb.utexas.edu/" target="_blank">http://www.rna.ccbb.utexas.edu/</a>. URL for 16S rRNA conservation diagram: <a href="http://www.rna.ccbb.utexas.edu/SAE/2B/ConsStruc/Diagrams/cons.16.3.3DOM.pdf" target="_blank">http://www.rna.ccbb.utexas.edu/SAE/2B/ConsStruc/Diagrams/cons.16.3.3DOM.pdf</a>]. Upper case colored nucleotides are conserved in at least 98% of the sequences used. For the <i>P. falciparum</i> mt rRNA fragments: red nucleotides match the 3P2O consensus sequence, light blue nucleotides differ, and black nucleotides cannot be compared to the consensus (which is conserved at less than 90%). Base pair symbols are colored when both of the paired nucleotides have the same color. Each fragment is labeled at its 5′ and 3′ ends. Each helix present in <i>P. falciparum</i> is labeled with its helix number in green (<i>e.g.</i>, H500), based on the CRW Site’s helix numbering system [URL: 16S rRNA, <a href="http://www.rna.ccbb.utexas.edu/CAR/1A/Structures/h.16.b.E.coli.hlxnum.pdf" target="_blank">http://www.rna.ccbb.utexas.edu/CAR/1A/Structures/h.16.b.E.coli.hlxnum.pdf</a>]. <b>Inset: </b><i>C. elegans</i> mt SSU rRNA secondary structure model.