Comparison of the reference (Rfam) structure of the Hammerhead Ribozyme and predicted structures. Two of the stems can not be predicted using the original RNAalifold. Better treatment of gaps is enough to predict all stems, but only using the RIBOSUM scoring scheme predicts all base pairs correctly.
Reference Structure of Hammerhead Ribozyme
identical to RIBOSUM predicted structure
Structure using the original RNAalifold
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Structure when using the new gap treatment
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When looking at the structure annotated alignment, one can see that the blue hairpin loop is much too long if the old RNAalifold is used, and therefore will not be formed. This in turn leads to a very long, energetically highly unfavorable interior loop between the green and the red stem. Thus, the red stem can also only be correctly predicted if gaps are not used to evaluate loop energies.
The two outer blue base pairs have so many counter examples that only the RIBOSUM way of giving a small bonus to identical base pairs also leads to their inclusion into the structure.
Z69690.1/342-390 GCCCCGCUGAUGAGGUCAG............................................................
Z69700.1/341-389 GCCCCGCUGAUGAGGUCAG............................................................
Z69693.1/343-391 GCCCUGCUGAUGAGGUCAG............................................................
Z69694.1/342-390 GCCCCGCUGAUGAGGUCAG............................................................
Z69701.1/341-389 GCCCCGCUGAUGAGGUCAG............................................................
Z69688.1/265-313 GCGCCGCUGAUGAGGUCAG............................................................
Z69699.1/341-389 GCCCCGCUGAUGAGGUCAG............................................................
Z69689.1/341-389 GCCCCGCUGGUGGGGUCAG............................................................
Z69697.1/341-389 GCCCCGCUGAUGAGGUCAG............................................................
Z69686.1/342-390 GCCCCGCUGAUGAGGUCAG............................................................
M19148.1/160-204 AUCCAACUGACCAGUCGGA............................................................
AF036745.1/119-163 AUCCAACUGACCAGUCGGA............................................................
L07513.1/84-40 AUCUAAAUGACGAGUCCUA............................................................
AF036398.1/58-102 AUCUUUCUGACGAGUUUCA............................................................
AF036755.1/118-162 AUCCNGCUGACGNGUCCCA............................................................
X15621.1/76-34 AUCCAGCUGACGAGUCCCA............................................................
AY028787.1/23621-23665 AUUUAGCUGACGAGUCCCA............................................................
L23117.1/1024-1069 CGACUGCUGAGGAGUCCCAC...........................................................
AF036743.1/118-165 AUUCAGCUGACGAGUCCCA............................................................
AF109181.1/634-589 GCAAUACUGAAGAGUUCCAC...........................................................
AF036390.1/118-165 AUCCAACUGACGAGUGCCC............................................................
X15620.1/19-62 GGCUAGCAGUGGAAUCC.A............................................................
AF036741.1/118-165 AUCCAGCCGACGAGUCCCA............................................................
AF036749.1/121-167 AUU.AACAGACGAGUCCCA............................................................
X15619.1/121-168 AUCCAGCUGACGAGUCCCA............................................................
AF036394.1/118-165 AUCCAGCUGACGUGUCCCA............................................................
AF036756.1/118-162 AUCCAGCUGACGAGUCCCA............................................................
AF036393.1/119-166 AUCCAGCUGACGAGUCCCA............................................................
AF036396.1/121-168 AUCCAACUGACGAGUGCCA............................................................
AF036397.1/119-166 AUCCAGCUGACGAGUCCCA............................................................
X15621.1/101-144 ACUCCG.UGACAAGUCUCG............................................................
AF213693.1/184-228 AUCCAACCGAUGAGUCCCA............................................................
AF036389.1/120-167 AUCCAGCUGACGAGUCCCA............................................................
D87492.1/743-788 GCACUGCUGAGGAGUCCCAC...........................................................
AF036746.1/113-157 AUCCAGCUGACCAGUCGGA............................................................
D87492.1/2147-2192 CAAUUGCUGAGGAGUCCCAU...........................................................
AF036750.1/119-165 AUCUAGCUGACGAGUCCCA............................................................
AF036748.1/120-164 AUCCAGCUGACGAGUCCUA............................................................
L07513.1/246-290 AUCUAGCUGACGAGUCCCG............................................................
AF036740.1/117-159 AUCCAGCUCACGAGUCCCA............................................................
AF036752.1/118-162 AUCCAGCUGACGAGUCCCA............................................................
AF036395.1/119-163 CCCUGGCUGACGAGUCCCA............................................................
AF036747.1/117-160 AUCCAGCUGACGAGUCCCA............................................................
AF036392.1/121-168 AUCCAACUGACGAGCGCCA............................................................
D87493.1/3564-3609 GCACUUCUGAAGAGUCCCAU...........................................................
AF036751.1/118-161 AUCCAGCUGACGAGUCCCA............................................................
AF213692.1/353-397 AUCCAGCCGAUGAGUUCCA............................................................
AF036391.1/121-168 AUCCAACUGACGAGUGCCA............................................................
D87492.1/1479-1524 AUCCAGUUGAUGAGUCCCAG...........................................................
AF036754.1/91-138 AUCCAGUUGACGAGUCCCA............................................................
AF036404.1/122-166 AUCCAGCUGACGAGUGCCA............................................................
AF036401.1/123-167 AUCCAGCUGACGAGUCCCA............................................................
AF036400.1/123-167 AUCCAGCUGACGAGUGCCA............................................................
AF036402.1/123-167 AUCCAGCUGACGAGUGCCA............................................................
AF404059.1/70-187 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAAUAAAAAGUUCACCACGAC
AF404053.1/70-186 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAAGUUCACCACGACU
AF229821.1/180-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAAGUUCACCACGACU
AF404073.1/70-162 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAACGACUCCUCCUUCUCU.............
X52044.1/179-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAGUUCACCACGACUC
AF404031.1/70-184 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAAUAAAAGUUCACCACAACUCC
AF404029.1/178-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUCUAAUAAAAGUUCACCACGACUCC
AF404055.1/70-187 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAAAGUUCACCACGAC
AF404068.1/70-185 CUUUCCAUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAGUUCACCACGACUC
AF404052.1/70-187 CUUUCCCUGAAGUGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAAGUUCACCACGAC
AF404062.1/178-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACCAAUUUUUUUAAUAAAAGUUCACCACGACUCC
AF404061.1/70-185 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAGCUCACCACGACUC
AF404040.1/70-186 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAGUUCACCACGACU
X52041.1/178-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAAUAAAAGUUCACCACGACUCC
AF404051.1/70-186 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUAAAUAAAAAGUUCACCACGACU
AF404063.1/176-63 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGGAACUAAUUUUUUUAAUAAAAGUUCACCACGACUCCU
AF404041.1/70-183 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAUAAAAGUUCACCACGACUCCU
S74687.1/181-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUUUUUUAAAAAGUUCACCACAAC
AF404054.1/70-188 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAAGUUCACCACGAC
AF404067.1/70-184 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAACAAAAGUUCACCACGACUCC
AF404046.1/177-64 CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAAUAAAAGCUCACCACGACUCC
SS_cons ((((((.......((((..............................................................
Z69690.1/342-390 ............GGAAGACCGAA...AGUGUCGACUCUA...CGGG.GC
Z69700.1/341-389 ............GGAAAACCGAA...AGUGUCGACUCUA...CGGG.GC
Z69693.1/343-391 ............GGAAGACUGAA...AGUGUCGACUCUA...CGGG.GC
Z69694.1/342-390 ............GGAAGACCGAA...AGUGUCGACUCUA...CGGU.GC
Z69701.1/341-389 ............GGAAGACCGAA...AGUGUCGACUCAA...CGGG.GC
Z69688.1/265-313 ............GGAAGACCGAA...AGUGUCGACUCUA...UGGG.GC
Z69699.1/341-389 ............GGAAGACCGAA...AGUGUCGACUCUA...CAGG.GC
Z69689.1/341-389 ............GGAAGGCCGAA...AGUGUCGACUCUA...CGGG.GC
Z69697.1/341-389 ............GGAAGACUGAA...AGUGUCGACUCUA...CGGG.GC
Z69686.1/342-390 ............GGAAGACCGAA...AGUGUUGACUCUA...CGGG.GC
M19148.1/160-204 ............AAUUGGACGAA...ACGC....GCGUC...CUGG.AU
AF036745.1/119-163 ............AAUAGGACGAA...ACGC....GCGUC...CAGG.AU
L07513.1/84-40 ............AAUGGAACUAA...ACAC....AUGUG...UUUG.AU
AF036398.1/58-102 ............AAUAGGACGAA...ACGC....GUGUC...AUGG.AU
AF036755.1/118-162 ............AAUAGGACGGA...AGGC....GCGUC...CCGG.AU
X15621.1/76-34 ............AAUAAGACGA....ACGC....GCGU....CUGG.AU
AY028787.1/23621-23665 ............AACGGUACGAA...ACUG....GCGUC...CUUG.AU
L23117.1/1024-1069 ............AAUAGGGCGAU...ACGG....ACGUC...CAGU.GC
AF036743.1/118-165 ............AAUAGGACGAAGUGACGC....GCGUC...CUGG.AU
AF109181.1/634-589 ............AAUAGGACGAA...ACGG....CGAUC...CAGU.GU
AF036390.1/118-165 ............AAUAGGAGGAA...ACGC....GCGUCAAACUGC.AU
X15620.1/19-62 ............AAUAGGACGAA...ACGC....GCGUC...CUGG.AU
AF036741.1/118-165 ............AAUAAAACGAA...ACGC....GCGUCAAAGUGG.AU
AF036749.1/121-167 ............AAUAGGACGAAGUGACGC....GCGUC...CUGG.AU
X15619.1/121-168 ............AAUAGGACGAA...ACGC....UCGUCAAAAUGC.AU
AF036394.1/118-165 ............AACAGCACGAA...ACGC....GCGUCAAACUGC.AU
AF036756.1/118-162 ............AGUAGGACGAA...ACGC....GCGUC...CUGG.AU
AF036393.1/119-166 ............AACAGGACGAA...ACGA....GAGUCAAACUGC.AU
AF036396.1/121-168 ............AAUAGGAGGAA...ACGC....GCGUCAAACUGC.AG
AF036397.1/119-166 ............AACAGCACGAA...ACGC....GCGUCAAACUGC.AU
X15621.1/101-144 ............AAUAGGACGAA...AUGU....GCGUC...CUAG.AU
AF213693.1/184-228 ............AAUAGAACGAA...ACCU....GCGUC...CUGG.AU
AF036389.1/120-167 ............AACAGGACGAA...ACGC....GCGUCAAACUGC.AU
D87492.1/743-788 ............AAUAGGACGAA...ACGA....CCGUC...CAGU.AC
AF036746.1/113-157 ............AAUAGGACGAA...ACGC....GCGUC...CUGG.AU
D87492.1/2147-2192 ............AAUAGGACGAA...ACGG....CCGUC...CAGU.GC
AF036750.1/119-165 ............AAUAGGACGAA...AU.C....GCGUCAAACUGG.AU
AF036748.1/120-164 ............AAUAGGGUGAA...ACGC....GCGUC...CUGG.AU
L07513.1/246-290 ............AAUAGGAGGAA...GUGC....UCGUU...CAAU.AU
AF036740.1/117-159 ............AAUAGGACGAA...ACG......CGUC...CUCC.AU
AF036752.1/118-162 ............AAUAGGACUUG...ACGC....GCGUC...CUGG.AU
AF036395.1/119-163 ............AACAGGACGAA...ACGC....GCGUC...CUGG.AU
AF036747.1/117-160 ............AAUAGG.CGAA...ACGC....GCGUC...CUGG.AU
AF036392.1/121-168 ............AAUAGGAGGAA...ACGC....GCGUCAAACUGC.AU
D87493.1/3564-3609 ............GCUAGGACGAA...ACAG....CCUUC...CAGU.AC
AF036751.1/118-161 ............AAUAGGACGA....ACGC....ACUUC...CUAG.AU
AF213692.1/353-397 ............AACAGGACUAA...ACGC....GCUUC...UUGG.AU
AF036391.1/121-168 ............AAUAGGAGGAA...ACGC....GCGUCAAACUGC.AU
D87492.1/1479-1524 ............AGAAGGACGAA...ACGU....GCAUC...CUGG.AU
AF036754.1/91-138 ............AAUUGGACGAA...ACGC....GCGUCAAACUGG.AU
AF036404.1/122-166 ............AAUAGGACGAA...AUGC....GCAUC...CUGG.AU
AF036401.1/123-167 ............AAUAGGACGAA...AUGC....GCAUC...CUGG.AU
AF036400.1/123-167 ............AAUAGGACGAA...AUGU....GCAUC...CUGG.AU
AF036402.1/123-167 ............AAUACGACGAA...AUGC....GCAUC...CUGG.AU
AF404059.1/70-187 UCCUCCUUCUCUCACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404053.1/70-186 CCUCCUUCUCU.CACAAGUCGAA...ACUCA...GAGUC...GGCA.AG
AF229821.1/180-64 CCUCCUUCUCU.CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404073.1/70-162 ............CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
X52044.1/179-64 CUCCUUCUCU..CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404031.1/70-184 UCCUUCUCU...CACAAGUCGAA...ACUCA...GAGUC...GGCG.AG
AF404029.1/178-64 UCCUUCUCU...CACAAGUCGAA...ACUCA...GAGUC...GGCA.AG
AF404055.1/70-187 UCCUCCUUCUCUCACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404068.1/70-185 CUCCUUCUCU..CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404052.1/70-187 UCCUCCUUCUCUCACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404062.1/178-64 UCCUUCUCU...CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404061.1/70-185 CUCCUUCUCU..CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404040.1/70-186 CCUCCUUCUCU.CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
X52041.1/178-64 UCCUUCUCU...CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404051.1/70-186 CCUCCUUCUCU.CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404063.1/176-63 CCUUCUCU....CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404041.1/70-183 CCUUCUCU....CACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
S74687.1/181-64 UCCUCCUUCUCUCACAAGUCGAA...ACUCA...GAGUC...GGAA.AG
AF404054.1/70-188 UCCUCCUUCUCUCACAAGUCGAA...ACUCA...GAGUC...GGAACAG
AF404067.1/70-184 UCCUUCUCU...CACAAGUCGAA...ACUCA...GAGUC...GGCA.AG
AF404046.1/177-64 UCCUUCUCU...CA.AAGUCGAA...ACUCA...GAGUC...GGGA.AG
SS_cons ................))))......((((....))))....)))).))