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Table 1 Distribution of Comparatively Predicted Secondary Structure Models Analyzed

From: Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

  5S rRNA 16S rRNA 23S rRNA tRNA Total
Structures 90 496 256 569 1,411
Total AGCU Nucleotides1 10,777 724,475 712,575 42,283 1,490,110
Total Nucleotides2 10,819 736,412 714,723 43,189 1,505,143
Total Comparative Pairings3 3,107 191,994 178,958 11,796 385,854
Average Sequence Length 120 1,485 2,792 76 -
Average Pairings/Structure3 35 387 699 21 -
Phylogenetic Distribution      
   Archaea 12 23 17 76 128
   Bacteria 28 195 75 155 453
   Eucarya      
Nuclear 45 133 52 207 437
Chloroplast 4 33 31 131 199
Mitochondrion 1 112 81 - 194
Pairwise Sequence Identity 4 Archaea Bacteria Nuclear Chloroplast Mitochondrion
   16S rRNA      
< 80% Identity 380 / 75% 32,456 / 86% 16,574 / 94% 746 / 71% 12,332 / 99%
< 50% Identity 0 / 0% 0 / 0% 8,500 / 48% 98 / 9% 9,852 / 79%
>= 95% Identity 16 / 3% 1,588 / 4% 212 / 1% 4 / 0.4% 12 / 0.1%
Total Pairs 506 37,830 17,556 1,056 12,432
   23S rRNA      
< 80% Identity 236 / 87% 5,214 / 94% 2,568 / 97% 710 / 76% 6,394 / 99%
< 50% Identity 0 / 0% 0 / 0% 1,960 / 74% 62 / 7% 5,830 / 90%
>= 95% Identity 6 / 2% 42 / 1% 8 / 0.30% 18 / 2% 8 / 0.1%
Total Pairs 272 5,550 2,652 930 6,480
tRNA Amino Acid Distribution 5 Archaea Bacteria Nuclear Chloroplast Total
   Alanine (Aln) 13 14 6 5 38
   Arginine (Arg) 4 9 17 12 42
   Asparagine (Asn) 3 9 10 3 25
   Aspartic acid (Asp) 4 4 12 6 26
   Cysteine (Cys) 2 5 3 5 15
   Glutamine (Gln) 3 6 13 4 26
   Glutamic acid (Glu) 4 8 23 8 43
   Glycine (Gly) 6 18 17 9 50
   Histidine (His) 3 6 10 7 26
   Isoleucine (Ile) 3 16 8 10 37
   Leucine (Leu) - - - - -
   Lysine (Lys) 3 8 15 4 30
   Methionine (Met) 4 7 7 9 27
   Phenylalanine (Phe) 3 6 16 10 35
   Proline (Pro) 5 10 12 8 35
   Serine (Ser) - - - - -
   Threonine (Thr) 7 14 6 10 37
   Tryptophan (Trp) 1 6 3 10 20
   Tyrosine (Tyr) 2 - 6 3 11
   Valine (Val) 6 9 23 8 46
Total 76 155 207 131 569
  1. 1 Considers only A, G, C or U nucleotides.
  2. 2 Considers all nucleotides.
  3. 3 Includes only G:C, A:U and G:U base-pairings predicted with comparative analysis.
  4. 4 Average sequence identities for all pairwise comparisons between sequences. Number of pairwise comparisons equals (n2-n) where n is the number of sequences considered.
  5. 5 Only Type I tRNAs are considered.