Motif Atlas Releases 0.11 and 0.12
Changes in PDB files used for clustering
Release 0.11 has 196 PDB files, release 0.12 has 196 PDB files, 196 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_93424.2 | 22 | tSH-inserted-tHW |
| 11 | IL_65553.4 | 22 | Kink-turn |
| 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_94430.3 | 15 | 16S h32-h33-h34 3WJ |
| 19 | IL_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 20 | IL_24982.3 | 15 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 21 | IL_49493.2 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 22 | IL_40090.2 | 11 | 16S h34 ILa : Part of larger motif |
| 23 | IL_46648.1 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 24 | IL_21304.1 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 25 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
| 26 | IL_24546.2 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 27 | IL_58291.2 | 9 | Recurrent Sub-motif found in junctions |
| 28 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 29 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 30 | IL_02809.1 | 8 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 31 | IL_92321.2 | 8 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 32 | IL_90459.2 | 8 | cWW AG or UU |
| 33 | IL_86357.2 | 7 | LSU Helix 61 IL2 |
| 34 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 35 | IL_73000.2 | 7 | cHS-cWS |
| 36 | IL_08926.1 | 6 | 23S H91 IL |
| 37 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
| 38 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
| 39 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
| 40 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
| 41 | IL_70237.3 | 6 | |
| 42 | IL_97057.2 | 6 | |
| 43 | IL_54420.1 | 6 | |
| 44 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
| 45 | IL_24022.2 | 6 | |
| 46 | IL_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 47 | IL_10007.1 | 6 | Single sheared with bulged bases |
| 48 | IL_79083.2 | 5 | |
| 49 | IL_92484.1 | 5 | |
| 50 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 51 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 52 | IL_77263.1 | 5 | Kink-turn from U4 |
| 53 | IL_90133.1 | 5 | |
| 54 | IL_01239.1 | 5 | |
| 55 | IL_02359.2 | 5 | |
| 56 | IL_45262.2 | 5 | |
| 57 | IL_78732.3 | 5 | Double S-turn motif |
| 58 | IL_39526.3 | 4 | |
| 59 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 60 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 61 | IL_40387.4 | 4 | LSU Helix 89 (H89) IL2 |
| 62 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 63 | IL_98556.3 | 4 | |
| 64 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 65 | IL_93568.1 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 66 | IL_10005.1 | 4 | |
| 67 | IL_21333.1 | 4 | tSH-tHW-bulge |
| 68 | IL_98591.2 | 4 | |
| 69 | IL_38807.2 | 4 | |
| 70 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 71 | IL_89028.3 | 3 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 72 | IL_95150.3 | 3 | |
| 73 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 74 | IL_16166.2 | 3 | |
| 75 | IL_23262.3 | 3 | |
| 76 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 77 | IL_62499.4 | 3 | |
| 78 | IL_98421.2 | 3 | SSU Helix 12 (h12) IL |
| 79 | IL_09348.3 | 3 | cWW-L-cWW-cWW |
| 80 | IL_16252.2 | 3 | 23S H91 IL |
| 81 | IL_30840.1 | 3 | |
| 82 | IL_34156.4 | 3 | cWW AG or UU |
| 83 | IL_52173.1 | 3 | |
| 84 | IL_58586.2 | 3 | |
| 85 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 86 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
| 87 | IL_43946.1 | 3 | |
| 88 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 89 | IL_91547.1 | 3 | tHS tHH bulge with S-turn |
| 90 | IL_34628.2 | 3 | Kink-turn |
| 91 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 92 | IL_36254.1 | 3 | |
| 93 | IL_71565.1 | 3 | |
| 94 | IL_75447.1 | 3 | |
| 95 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 96 | IL_45794.1 | 2 | |
| 97 | IL_54965.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. |
| 98 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 99 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 100 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 101 | IL_25174.1 | 2 | |
| 102 | IL_37197.1 | 2 | |
| 103 | IL_55287.1 | 2 | |
| 104 | IL_81441.1 | 2 | |
| 105 | IL_12211.1 | 2 | |
| 106 | IL_28942.1 | 2 | |
| 107 | IL_33965.1 | 2 | tHS tHH bulge with S-turn |
| 108 | IL_46435.1 | 2 | |
| 109 | IL_50521.1 | 2 | |
| 110 | IL_69901.1 | 2 | |
| 111 | IL_87336.1 | 2 | LSU Eukaryal Helix 96 (H96) IL1 |
| 112 | IL_89231.1 | 2 | LSU H77 |
| 113 | IL_23414.1 | 2 | |
| 114 | IL_37406.1 | 2 | |
| 115 | IL_77076.1 | 2 | |
| 116 | IL_91132.1 | 2 | |
| 117 | IL_00998.1 | 2 | |
| 118 | IL_09882.1 | 2 | |
| 119 | IL_16330.1 | 2 | |
| 120 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 121 | IL_58811.1 | 2 | |
| 122 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 123 | IL_74876.1 | 2 | |
| 124 | IL_80093.1 | 2 | |
| 125 | IL_87548.1 | 2 | |
| 126 | IL_90057.1 | 2 | |
| 127 | IL_98566.1 | 2 | |
| 128 | IL_01054.1 | 2 | |
| 129 | IL_16377.1 | 2 | |
| 130 | IL_40892.1 | 2 | |
| 131 | IL_52940.1 | 2 | |
| 132 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 133 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 134 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 135 | IL_21495.1 | 2 | |
| 136 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 137 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 138 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 139 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
| 140 | IL_97833.1 | 2 | |
| 141 | IL_07300.1 | 2 | |
| 142 | IL_11751.1 | 2 | |
| 143 | IL_47968.1 | 1 | |
| 144 | IL_53423.1 | 1 | |
| 145 | IL_57977.1 | 1 | |
| 146 | IL_61730.1 | 1 | |
| 147 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 148 | IL_71942.1 | 1 | |
| 149 | IL_81398.1 | 1 | |
| 150 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 151 | IL_91044.1 | 1 | |
| 152 | IL_92280.1 | 1 | |
| 153 | IL_97842.1 | 1 | |
| 154 | IL_98924.1 | 1 | |
| 155 | IL_06306.1 | 1 | |
| 156 | IL_11869.1 | 1 | |
| 157 | IL_18755.1 | 1 | |
| 158 | IL_41791.1 | 1 | |
| 159 | IL_46306.1 | 1 | |
| 160 | IL_61991.1 | 1 | |
| 161 | IL_67735.1 | 1 | |
| 162 | IL_76256.1 | 1 | |
| 163 | IL_78809.1 | 1 | |
| 164 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 165 | IL_91078.1 | 1 | |
| 166 | IL_97961.1 | 1 | |
| 167 | IL_02835.1 | 1 | |
| 168 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 169 | IL_20775.1 | 1 | tSH-inserted |
| 170 | IL_25181.1 | 1 | |
| 171 | IL_37347.1 | 1 | |
| 172 | IL_41864.1 | 1 | Part of H71 junction in 23S rRNA from T.th. |
| 173 | IL_55649.1 | 1 | |
| 174 | IL_58454.1 | 1 | |
| 175 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 176 | IL_82113.1 | 1 | |
| 177 | IL_83856.1 | 1 | |
| 178 | IL_91089.1 | 1 | |
| 179 | IL_96031.1 | 1 | tHS tHH bulge with S-turn |
| 180 | IL_02957.1 | 1 | |
| 181 | IL_12486.1 | 1 | |
| 182 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 183 | IL_40527.1 | 1 | Kink-turn |
| 184 | IL_43316.1 | 1 | |
| 185 | IL_53988.1 | 1 | |
| 186 | IL_55934.1 | 1 | kink-turn-like |
| 187 | IL_83920.1 | 1 | |
| 188 | IL_87544.1 | 1 | |
| 189 | IL_89794.1 | 1 | |
| 190 | IL_03110.1 | 1 | |
| 191 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 192 | IL_12507.1 | 1 | |
| 193 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 194 | IL_37715.1 | 1 | |
| 195 | IL_40845.1 | 1 | |
| 196 | IL_52509.1 | 1 | |
| 197 | IL_63952.1 | 1 | |
| 198 | IL_77195.1 | 1 | |
| 199 | IL_85510.1 | 1 | |
| 200 | IL_97073.1 | 1 | |
| 201 | IL_03282.1 | 1 | |
| 202 | IL_06471.1 | 1 | |
| 203 | IL_25307.1 | 1 | |
| 204 | IL_31241.1 | 1 | |
| 205 | IL_37990.1 | 1 | |
| 206 | IL_54450.1 | 1 | |
| 207 | IL_59529.1 | 1 | |
| 208 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 209 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 210 | IL_91904.1 | 1 | |
| 211 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 212 | IL_03741.1 | 1 | |
| 213 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 214 | IL_13682.1 | 1 | |
| 215 | IL_21421.1 | 1 | |
| 216 | IL_26868.1 | 1 | |
| 217 | IL_41139.1 | 1 | |
| 218 | IL_47687.1 | 1 | |
| 219 | IL_52958.1 | 1 | |
| 220 | IL_54576.1 | 1 | |
| 221 | IL_56513.1 | 1 | |
| 222 | IL_60643.1 | 1 | |
| 223 | IL_77296.1 | 1 | |
| 224 | IL_80505.1 | 1 | |
| 225 | IL_82650.1 | 1 | |
| 226 | IL_85805.1 | 1 | |
| 227 | IL_88367.1 | 1 | |
| 228 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 229 | IL_05221.1 | 1 | |
| 230 | IL_06847.1 | 1 | Group II Intron IL |
| 231 | IL_11302.1 | 1 | |
| 232 | IL_17603.1 | 1 | |
| 233 | IL_26971.1 | 1 | |
| 234 | IL_53323.1 | 1 | |
| 235 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 236 | IL_60649.1 | 1 | Kink-turn |
| 237 | IL_65788.1 | 1 | |
| 238 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 239 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 240 | IL_80652.1 | 1 | |
| 241 | IL_86059.1 | 1 | |
| 242 | IL_88403.1 | 1 | |
| 243 | IL_90880.1 | 1 | |
| 244 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 245 | IL_98688.1 | 1 | |
| 246 | IL_02690.1 | 1 | |
| 247 | IL_05462.1 | 1 | |
| 248 | IL_15205.1 | 1 | |
| 249 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 250 | IL_22579.1 | 1 | |
| 251 | IL_25082.1 | 1 | |
| 252 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 253 | IL_37150.1 | 1 | tHS tHH bulge with S-turn |
| 254 | IL_39324.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|