Kink-Switch Motifs in 23S rRNA Identified by Automated Methods

Cocked Kink-Switch residue #s sequence coordinates comment
22 22-25
518-521		 5' UGGA 3'
3' AAAG 5'		 [] yes
365 365-368
282-287		 5' GUGC 3'
3' CUACUCU 5'		 [] ??
439 439-442
40-41,185		 5' ACAA 3'
3' CG,G 5'		 [] ??
793 793-796
817-821		 5' AUG_A 3'
3' GAAGU 5'		 [] ??
815 815-818
795-798		 5' UGGA 3'
3' GAAG 5'		 [] yes
2501 2501-2504
2516-2519		 5' GCAA 3'
3' CCAG 5'		 [] yes
Tripped Kink Switch residue #s sequence coordinates KSMS
1 42-50
111-114,148-149		 GCGAUGAAG
CGAAAG		 [] not named
2 92-100
77-82		 GCGAAGAAC
GGGAGC		 [] Kt-7
3 259-267
244-250		 GCAAUGUGG
CCGAAGC		 [] Kt-15
4 882-889
772-774,2113,868,1837,1689		 AUCGAGUC*
GACGGGA		 [] ??
5 1025-1034
936-941		 CUGUUUGACG*
CCGAGG		 [] Kt-38
6 1146-1154
1213-1217		 CCCUAGACA*
CGAGG		 [] Kt-42
7 1311-1319
1338-1343		 GGAUGGAAG*
UGGACC		 [] Kt-46
8 1601-1608
1587-1593		 GCAGGAAG*
CGGAAGC		 [] Kt-58
*the conformation of the residues in italic are variable.
?? indicates an outlier, not a legitimate Kink-Switch