Pyrococcus sRNA Annotation

None of the Pyrococcus predictions have been verified as RNA transcripts by primer extension. Pho, Pfu, Pab Columns: "+" in these columns indicate the target described in the row occurs in the respective species. A blank indicates the target was not found, and an "X" indicates the homologous sRNA was not found in the species. Guide Box: the position of the guide within the sRNA (D or D' box associated). A D'' box is noted for sR55, which appears to be a third guide region, between the D' box and D box. This prediction is based on strong conservation of the unusually long mid-sRNA linker region (see the Pyrococcus alignment). Target RNA: predicted target of methylation. Target Position: predicted nucleotide postion of methylation. Nucleotide numbering is identical for 16S rRNA for all three species.  Pho rRNA numbering is used for 23S rRNA target sites.  See tables below for nucleotide numbering adjustments for Pfu or Pab 23S rRNA target sites.  tRNA positions noted use canonical tRNA numbering (i.e., anticodon is always N34-N36).  Match/Mismatch: the number of Watson-Crick and G-U matches / mismatches within the sRNA-target RNA duplex. "??" - no strong prediction found. When the three Pyrococcus sRNAs have different Match/Mismatch values, all three are listed in the order of P.hori, P.furi, P.abys.