Motif Atlas Releases 0.11 and 0.12
Changes in PDB files used for clustering
Release 0.11 has 197 PDB files, release 0.12 has 197 PDB files, 197 of them are identical.
No equivalence class representatives have been replaced.
No new PDB files have been added.
No equivalence class representatives have been obsoleted.
Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.
Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.
PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.
Redistribution of motif instances
Changes in motif groups
Release 0.11 has 266 motif groups, release 0.12 has 266 motif groups, 266 of them are identical.
0 motif groups were updated, 0 groups are present only in release 0.11, 0 groups are only in release 0.12.
Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:
Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey
Hover over the links connecting the motif groups to see which motif instances were exchanged.
Identical motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_97217.4 | 235 | 1-3 bulged nucleotides, same chain |
| 2 | IL_47174.5 | 203 | cWW AG or water inserted cWW Y-Y. |
| 3 | IL_39199.2 | 55 | Hoogsteen-edge Platform, Single bulged base |
| 4 | IL_41766.2 | 49 | Tandem cWW pairs (Not AU or GC) |
| 5 | IL_56465.2 | 45 | Single, unpaired intercalated base, consensus A |
| 6 | IL_44540.2 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 7 | IL_87904.3 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 8 | IL_06390.1 | 25 | cWH basepair with syn base |
| 9 | IL_13959.2 | 24 | Double Sheared (tSH-tHS) |
| 10 | IL_65553.4 | 22 | Kink-turn |
| 11 | IL_93424.2 | 22 | tSH-inserted-tHW |
| 12 | IL_32390.2 | 21 | 16S h19 IL and 23S H41 IL |
| 13 | IL_73276.1 | 20 | C-loop |
| 14 | IL_55938.2 | 19 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 15 | IL_92027.2 | 17 | 16S h21 S8 binding site |
| 16 | IL_06429.2 | 16 | cWW-bulge-cWW |
| 17 | IL_85647.2 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 18 | IL_24982.3 | 15 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 19 | IL_94430.3 | 15 | 16S h32-h33-h34 3WJ |
| 20 | IL_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 21 | IL_49493.2 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 22 | IL_21304.1 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 23 | IL_40090.2 | 11 | 16S h34 ILa : Part of larger motif |
| 24 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
| 25 | IL_46648.1 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 26 | IL_24546.2 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 27 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 28 | IL_58291.2 | 9 | Recurrent Sub-motif found in junctions |
| 29 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 30 | IL_92321.2 | 8 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 31 | IL_02809.1 | 8 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 32 | IL_90459.2 | 8 | cWW AG or UU |
| 33 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 34 | IL_73000.2 | 7 | cHS-cWS |
| 35 | IL_86357.2 | 7 | LSU Helix 61 IL2 |
| 36 | IL_10007.1 | 6 | Single sheared with bulged bases |
| 37 | IL_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 38 | IL_97057.2 | 6 | |
| 39 | IL_08926.1 | 6 | 23S H91 IL |
| 40 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
| 41 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
| 42 | IL_70237.3 | 6 | |
| 43 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
| 44 | IL_24022.2 | 6 | |
| 45 | IL_54420.1 | 6 | |
| 46 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
| 47 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
| 48 | IL_45262.2 | 5 | |
| 49 | IL_77263.1 | 5 | Kink-turn from U4 |
| 50 | IL_01239.1 | 5 | |
| 51 | IL_90133.1 | 5 | |
| 52 | IL_92484.1 | 5 | |
| 53 | IL_79083.2 | 5 | |
| 54 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 55 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 56 | IL_78732.3 | 5 | Double S-turn motif |
| 57 | IL_02359.2 | 5 | |
| 58 | IL_21333.1 | 4 | tSH-tHW-bulge |
| 59 | IL_98556.3 | 4 | |
| 60 | IL_38807.2 | 4 | |
| 61 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 62 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 63 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 64 | IL_10005.1 | 4 | |
| 65 | IL_98591.2 | 4 | |
| 66 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 67 | IL_93568.1 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 68 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 69 | IL_40387.4 | 4 | LSU Helix 89 (H89) IL2 |
| 70 | IL_39526.3 | 4 | |
| 71 | IL_62499.4 | 3 | |
| 72 | IL_34156.4 | 3 | cWW AG or UU |
| 73 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 74 | IL_16166.2 | 3 | |
| 75 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
| 76 | IL_43946.1 | 3 | |
| 77 | IL_23262.3 | 3 | |
| 78 | IL_52173.1 | 3 | |
| 79 | IL_36254.1 | 3 | |
| 80 | IL_09348.3 | 3 | cWW-L-cWW-cWW |
| 81 | IL_98421.2 | 3 | SSU Helix 12 (h12) IL |
| 82 | IL_58586.2 | 3 | |
| 83 | IL_75447.1 | 3 | |
| 84 | IL_16252.2 | 3 | 23S H91 IL |
| 85 | IL_95150.3 | 3 | |
| 86 | IL_71565.1 | 3 | |
| 87 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 88 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 89 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 90 | IL_89028.3 | 3 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 91 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 92 | IL_30840.1 | 3 | |
| 93 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 94 | IL_34628.2 | 3 | Kink-turn |
| 95 | IL_91547.1 | 3 | tHS tHH bulge with S-turn |
| 96 | IL_11751.1 | 2 | |
| 97 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 98 | IL_91132.1 | 2 | |
| 99 | IL_21495.1 | 2 | |
| 100 | IL_33965.1 | 2 | tHS tHH bulge with S-turn |
| 101 | IL_74876.1 | 2 | |
| 102 | IL_45794.1 | 2 | |
| 103 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 104 | IL_97833.1 | 2 | |
| 105 | IL_37406.1 | 2 | |
| 106 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 107 | IL_69901.1 | 2 | |
| 108 | IL_25174.1 | 2 | |
| 109 | IL_16377.1 | 2 | |
| 110 | IL_16330.1 | 2 | |
| 111 | IL_96446.1 | 2 | |
| 112 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 113 | IL_98566.1 | 2 | |
| 114 | IL_01054.1 | 2 | |
| 115 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 116 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 117 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 118 | IL_40892.1 | 2 | |
| 119 | IL_58811.1 | 2 | |
| 120 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 121 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 122 | IL_87336.1 | 2 | LSU Eukaryal Helix 96 (H96) IL1 |
| 123 | IL_81441.1 | 2 | |
| 124 | IL_89231.1 | 2 | LSU H77 |
| 125 | IL_54965.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. |
| 126 | IL_80093.1 | 2 | |
| 127 | IL_00998.1 | 2 | |
| 128 | IL_55287.1 | 2 | |
| 129 | IL_50521.1 | 2 | |
| 130 | IL_09882.1 | 2 | |
| 131 | IL_77076.1 | 2 | |
| 132 | IL_46435.1 | 2 | |
| 133 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
| 134 | IL_28942.1 | 2 | |
| 135 | IL_87548.1 | 2 | |
| 136 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 137 | IL_52940.1 | 2 | |
| 138 | IL_90057.1 | 2 | |
| 139 | IL_12211.1 | 2 | |
| 140 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 141 | IL_23414.1 | 2 | |
| 142 | IL_07300.1 | 2 | |
| 143 | IL_37197.1 | 2 | |
| 144 | IL_63952.1 | 1 | |
| 145 | IL_80505.1 | 1 | |
| 146 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 147 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 148 | IL_97073.1 | 1 | |
| 149 | IL_12486.1 | 1 | |
| 150 | IL_31241.1 | 1 | |
| 151 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 152 | IL_06306.1 | 1 | |
| 153 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 154 | IL_37990.1 | 1 | |
| 155 | IL_90880.1 | 1 | |
| 156 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 157 | IL_23448.1 | 1 | |
| 158 | IL_57285.1 | 1 | |
| 159 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 160 | IL_82650.1 | 1 | |
| 161 | IL_61991.1 | 1 | |
| 162 | IL_47687.1 | 1 | |
| 163 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 164 | IL_54450.1 | 1 | |
| 165 | IL_76256.1 | 1 | |
| 166 | IL_83856.1 | 1 | |
| 167 | IL_97842.1 | 1 | |
| 168 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 169 | IL_17603.1 | 1 | |
| 170 | IL_15205.1 | 1 | |
| 171 | IL_60643.1 | 1 | |
| 172 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 173 | IL_40845.1 | 1 | |
| 174 | IL_88865.1 | 1 | |
| 175 | IL_76263.1 | 1 | |
| 176 | IL_25307.1 | 1 | |
| 177 | IL_55649.1 | 1 | |
| 178 | IL_52509.1 | 1 | |
| 179 | IL_22579.1 | 1 | |
| 180 | IL_77014.1 | 1 | |
| 181 | IL_03741.1 | 1 | |
| 182 | IL_81398.1 | 1 | |
| 183 | IL_37347.1 | 1 | |
| 184 | IL_46306.1 | 1 | |
| 185 | IL_41864.1 | 1 | Part of H71 junction in 23S rRNA from T.th. |
| 186 | IL_91044.1 | 1 | |
| 187 | IL_27668.1 | 1 | |
| 188 | IL_92280.1 | 1 | |
| 189 | IL_91379.1 | 1 | |
| 190 | IL_26868.1 | 1 | |
| 191 | IL_89794.1 | 1 | |
| 192 | IL_37150.1 | 1 | tHS tHH bulge with S-turn |
| 193 | IL_37715.1 | 1 | |
| 194 | IL_55934.1 | 1 | kink-turn-like |
| 195 | IL_27243.1 | 1 | |
| 196 | IL_71942.1 | 1 | |
| 197 | IL_91078.1 | 1 | |
| 198 | IL_82113.1 | 1 | |
| 199 | IL_05221.1 | 1 | |
| 200 | IL_06471.1 | 1 | |
| 201 | IL_56513.1 | 1 | |
| 202 | IL_85510.1 | 1 | |
| 203 | IL_06847.1 | 1 | Group II Intron IL |
| 204 | IL_02835.1 | 1 | |
| 205 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 206 | IL_96031.1 | 1 | tHS tHH bulge with S-turn |
| 207 | IL_11302.1 | 1 | |
| 208 | IL_53988.1 | 1 | |
| 209 | IL_61730.1 | 1 | |
| 210 | IL_75328.1 | 1 | |
| 211 | IL_87544.1 | 1 | |
| 212 | IL_25082.1 | 1 | |
| 213 | IL_53323.1 | 1 | |
| 214 | IL_26971.1 | 1 | |
| 215 | IL_91904.1 | 1 | |
| 216 | IL_21421.1 | 1 | |
| 217 | IL_88367.1 | 1 | |
| 218 | IL_60649.1 | 1 | Kink-turn |
| 219 | IL_85805.1 | 1 | |
| 220 | IL_03110.1 | 1 | |
| 221 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 222 | IL_98688.1 | 1 | |
| 223 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 224 | IL_05462.1 | 1 | |
| 225 | IL_20775.1 | 1 | tSH-inserted |
| 226 | IL_65788.1 | 1 | |
| 227 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 228 | IL_78809.1 | 1 | |
| 229 | IL_53423.1 | 1 | |
| 230 | IL_77195.1 | 1 | |
| 231 | IL_98924.1 | 1 | |
| 232 | IL_59529.1 | 1 | |
| 233 | IL_02957.1 | 1 | |
| 234 | IL_58454.1 | 1 | |
| 235 | IL_40527.1 | 1 | Kink-turn |
| 236 | IL_77296.1 | 1 | |
| 237 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 238 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 239 | IL_41791.1 | 1 | |
| 240 | IL_43316.1 | 1 | |
| 241 | IL_83920.1 | 1 | |
| 242 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 243 | IL_11869.1 | 1 | |
| 244 | IL_54576.1 | 1 | |
| 245 | IL_13682.1 | 1 | |
| 246 | IL_67735.1 | 1 | |
| 247 | IL_97961.1 | 1 | |
| 248 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 249 | IL_25181.1 | 1 | |
| 250 | IL_47968.1 | 1 | |
| 251 | IL_18755.1 | 1 | |
| 252 | IL_41139.1 | 1 | |
| 253 | IL_03282.1 | 1 | |
| 254 | IL_57977.1 | 1 | |
| 255 | IL_39324.1 | 1 | |
| 256 | IL_86059.1 | 1 | |
| 257 | IL_12507.1 | 1 | |
| 258 | IL_88403.1 | 1 | |
| 259 | IL_52958.1 | 1 | |
| 260 | IL_80652.1 | 1 | |
| 261 | IL_02690.1 | 1 | |
| 262 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 263 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 264 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 265 | IL_91089.1 | 1 | |
| 266 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
Updated motif groups
| # | Motif id | Instances | Description |
|---|
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|