Motif Atlas Releases 1.2 and 1.3
Changes in PDB files used for clustering
Release 1.2 has 201 PDB files, release 1.3 has 201 PDB files, 201 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 1.2 has 271 motif groups, release 1.3 has 271 motif groups, 271 of them are identical.
0 motif groups were updated, 0 groups are present only in release 1.2, 0 groups are only in release 1.3.
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_97217.6 | 239 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_47174.6 | 201 | cWW AG or water inserted cWW Y-Y. |
| 3 | IL_39199.3 | 54 | Hoogsteen-edge Platform, Single bulged base |
| 4 | IL_41766.3 | 49 | Tandem cWW pairs (Not AU or GC) |
| 5 | IL_56465.3 | 46 | Single, unpaired intercalated base, consensus A |
| 6 | IL_44540.3 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 7 | IL_87904.4 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 8 | IL_06390.3 | 26 | cWH basepair with syn base |
| 9 | IL_13959.3 | 24 | Double Sheared (tSH-tHS) |
| 10 | IL_93424.3 | 22 | tSH-inserted-tHW |
| 11 | IL_65553.5 | 22 | Kink-turn |
| 12 | IL_73276.3 | 21 | C-loop |
| 13 | IL_28947.1 | 21 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 14 | IL_55938.3 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 15 | IL_92027.3 | 17 | 16S h21 S8 binding site |
| 16 | IL_24982.4 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 17 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 18 | IL_92109.1 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 19 | IL_94430.4 | 15 | 16S h32-h33-h34 3WJ |
| 20 | IL_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 21 | IL_49493.3 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 22 | IL_40090.3 | 11 | 16S h34 ILa : Part of larger motif |
| 23 | IL_43124.1 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 24 | IL_21304.2 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 25 | IL_46648.2 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 26 | IL_24546.3 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 27 | IL_02809.2 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 28 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 29 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 30 | IL_58291.3 | 9 | Recurrent Sub-motif found in junctions |
| 31 | IL_90459.3 | 9 | cWW AG or UU |
| 32 | IL_92321.3 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 33 | IL_73000.2 | 7 | cHS-cWS |
| 34 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 35 | IL_44067.3 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 36 | IL_97057.3 | 6 | |
| 37 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 38 | IL_90133.2 | 6 | |
| 39 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 40 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 41 | IL_54420.1 | 6 | |
| 42 | IL_70237.3 | 6 | |
| 43 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 44 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 45 | IL_77263.1 | 5 | Kink-turn from U4 |
| 46 | IL_45262.3 | 5 | |
| 47 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 48 | IL_16207.1 | 5 | Single sheared with bulged bases |
| 49 | IL_08926.2 | 5 | 23S H91 IL |
| 50 | IL_79083.3 | 5 | |
| 51 | IL_92484.1 | 5 | |
| 52 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 53 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 54 | IL_78732.3 | 5 | Double S-turn motif |
| 55 | IL_02359.3 | 5 | |
| 56 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 57 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 58 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 59 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 60 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 61 | IL_42251.1 | 4 | |
| 62 | IL_38807.3 | 4 | |
| 63 | IL_01080.1 | 4 | |
| 64 | IL_16166.3 | 4 | 23S H91 IL |
| 65 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 66 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 67 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 68 | IL_98591.3 | 4 | |
| 69 | IL_94403.1 | 4 | LSU H77 |
| 70 | IL_08559.1 | 4 | LSU Helix 89 (H89) IL2 |
| 71 | IL_39526.4 | 4 | |
| 72 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 73 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 74 | IL_92267.1 | 3 | 23S H73 ILa : Part of larger Motif |
| 75 | IL_48918.2 | 3 | Kink-turn variant |
| 76 | IL_80348.1 | 3 | 23S H91 IL |
| 77 | IL_34156.6 | 3 | cWW AG or UU |
| 78 | IL_10647.1 | 3 | tHS tHH bulge with S-turn |
| 79 | IL_98421.3 | 3 | SSU Helix 12 (h12) IL |
| 80 | IL_52173.1 | 3 | |
| 81 | IL_43946.1 | 3 | |
| 82 | IL_09520.2 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 83 | IL_56077.1 | 3 | |
| 84 | IL_34628.2 | 3 | Kink-turn |
| 85 | IL_95150.3 | 3 | |
| 86 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 87 | IL_75447.1 | 3 | |
| 88 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 89 | IL_58586.2 | 3 | |
| 90 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 91 | IL_05723.1 | 3 | |
| 92 | IL_62499.6 | 3 | |
| 93 | IL_71565.3 | 3 | |
| 94 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 95 | IL_89028.5 | 3 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 96 | IL_30840.1 | 3 | |
| 97 | IL_19898.1 | 2 | |
| 98 | IL_90057.1 | 2 | |
| 99 | IL_12211.1 | 2 | |
| 100 | IL_21495.1 | 2 | |
| 101 | IL_09901.1 | 2 | tHS tHH bulge with S-turn |
| 102 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 103 | IL_33925.1 | 2 | |
| 104 | IL_01054.1 | 2 | |
| 105 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 106 | IL_37406.1 | 2 | |
| 107 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 108 | IL_28942.1 | 2 | |
| 109 | IL_23414.1 | 2 | |
| 110 | IL_37197.1 | 2 | |
| 111 | IL_97833.1 | 2 | |
| 112 | IL_23262.4 | 2 | |
| 113 | IL_07300.1 | 2 | |
| 114 | IL_45794.1 | 2 | |
| 115 | IL_33964.1 | 2 | |
| 116 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 117 | IL_98566.1 | 2 | |
| 118 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 119 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 120 | IL_24358.1 | 2 | |
| 121 | IL_16330.1 | 2 | |
| 122 | IL_50521.1 | 2 | |
| 123 | IL_40892.1 | 2 | |
| 124 | IL_87548.1 | 2 | |
| 125 | IL_09882.1 | 2 | |
| 126 | IL_91273.1 | 2 | |
| 127 | IL_00998.1 | 2 | |
| 128 | IL_16252.3 | 2 | 23S H91 IL |
| 129 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 130 | IL_49550.1 | 2 | tHS tHH bulge with S-turn |
| 131 | IL_96446.1 | 2 | |
| 132 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 133 | IL_52940.1 | 2 | |
| 134 | IL_09348.5 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 135 | IL_80093.1 | 2 | |
| 136 | IL_46435.1 | 2 | |
| 137 | IL_09587.1 | 2 | |
| 138 | IL_27892.1 | 2 | |
| 139 | IL_88180.1 | 2 | cWW-bulge-cWW |
| 140 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 141 | IL_11751.1 | 2 | |
| 142 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 143 | IL_77076.1 | 2 | |
| 144 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 145 | IL_55287.1 | 2 | |
| 146 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 147 | IL_57977.1 | 1 | |
| 148 | IL_39324.1 | 1 | |
| 149 | IL_80505.1 | 1 | |
| 150 | IL_47687.1 | 1 | |
| 151 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 152 | IL_97073.1 | 1 | |
| 153 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 154 | IL_78809.1 | 1 | |
| 155 | IL_13682.1 | 1 | |
| 156 | IL_31290.1 | 1 | |
| 157 | IL_13434.1 | 1 | |
| 158 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 159 | IL_25181.1 | 1 | |
| 160 | IL_58454.1 | 1 | |
| 161 | IL_40527.1 | 1 | Kink-turn |
| 162 | IL_60649.1 | 1 | Kink-turn |
| 163 | IL_52610.1 | 1 | |
| 164 | IL_40845.1 | 1 | |
| 165 | IL_86059.1 | 1 | |
| 166 | IL_82650.1 | 1 | |
| 167 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 168 | IL_21221.1 | 1 | SSU Helix 12 (h12) IL |
| 169 | IL_54576.1 | 1 | |
| 170 | IL_67735.1 | 1 | |
| 171 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 172 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 173 | IL_64589.1 | 1 | |
| 174 | IL_41139.1 | 1 | |
| 175 | IL_77296.1 | 1 | |
| 176 | IL_87394.1 | 1 | |
| 177 | IL_25307.1 | 1 | |
| 178 | IL_26868.1 | 1 | |
| 179 | IL_55649.1 | 1 | |
| 180 | IL_52509.1 | 1 | |
| 181 | IL_02690.1 | 1 | |
| 182 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 183 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 184 | IL_37990.1 | 1 | |
| 185 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 186 | IL_34868.1 | 1 | LSU Eukaryal Helix 96 (H96) IL1 |
| 187 | IL_03282.1 | 1 | |
| 188 | IL_42891.1 | 1 | |
| 189 | IL_88865.1 | 1 | |
| 190 | IL_76263.1 | 1 | |
| 191 | IL_91379.1 | 1 | |
| 192 | IL_11302.1 | 1 | |
| 193 | IL_89794.1 | 1 | |
| 194 | IL_95774.1 | 1 | tHS tHH bulge with S-turn |
| 195 | IL_12486.1 | 1 | |
| 196 | IL_06306.1 | 1 | |
| 197 | IL_97842.1 | 1 | |
| 198 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 199 | IL_17603.1 | 1 | |
| 200 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 201 | IL_91089.1 | 1 | |
| 202 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 203 | IL_47732.1 | 1 | |
| 204 | IL_85805.1 | 1 | |
| 205 | IL_92280.1 | 1 | |
| 206 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 207 | IL_04550.1 | 1 | tHS tHH bulge with S-turn |
| 208 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 209 | IL_53988.1 | 1 | |
| 210 | IL_28644.1 | 1 | |
| 211 | IL_11778.1 | 1 | |
| 212 | IL_37715.1 | 1 | |
| 213 | IL_54450.1 | 1 | |
| 214 | IL_77014.1 | 1 | |
| 215 | IL_03741.1 | 1 | |
| 216 | IL_83856.1 | 1 | |
| 217 | IL_37347.1 | 1 | |
| 218 | IL_46306.1 | 1 | |
| 219 | IL_15674.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 220 | IL_15205.1 | 1 | |
| 221 | IL_23448.1 | 1 | |
| 222 | IL_57285.1 | 1 | |
| 223 | IL_30354.1 | 1 | |
| 224 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 225 | IL_02835.1 | 1 | |
| 226 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 227 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 228 | IL_05462.1 | 1 | |
| 229 | IL_20775.1 | 1 | tSH-inserted |
| 230 | IL_71942.1 | 1 | |
| 231 | IL_91078.1 | 1 | |
| 232 | IL_81398.1 | 1 | |
| 233 | IL_05221.1 | 1 | |
| 234 | IL_06471.1 | 1 | |
| 235 | IL_91904.1 | 1 | |
| 236 | IL_56513.1 | 1 | |
| 237 | IL_60643.1 | 1 | |
| 238 | IL_46721.1 | 1 | |
| 239 | IL_63952.1 | 1 | |
| 240 | IL_03110.1 | 1 | |
| 241 | IL_83920.1 | 1 | |
| 242 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 243 | IL_27243.1 | 1 | |
| 244 | IL_75328.1 | 1 | |
| 245 | IL_82113.1 | 1 | |
| 246 | IL_53323.1 | 1 | |
| 247 | IL_26971.1 | 1 | |
| 248 | IL_09491.1 | 1 | |
| 249 | IL_21421.1 | 1 | |
| 250 | IL_85510.1 | 1 | |
| 251 | IL_91044.1 | 1 | |
| 252 | IL_27668.1 | 1 | |
| 253 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 254 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 255 | IL_41791.1 | 1 | |
| 256 | IL_43316.1 | 1 | |
| 257 | IL_12507.1 | 1 | |
| 258 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 259 | IL_52958.1 | 1 | |
| 260 | IL_80652.1 | 1 | |
| 261 | IL_65788.1 | 1 | |
| 262 | IL_61730.1 | 1 | |
| 263 | IL_41341.1 | 1 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 264 | IL_25082.1 | 1 | |
| 265 | IL_98924.1 | 1 | |
| 266 | IL_59529.1 | 1 | |
| 267 | IL_02957.1 | 1 | |
| 268 | IL_28468.1 | 1 | Single sheared with bulged bases |
| 269 | IL_88367.1 | 1 | |
| 270 | IL_06847.1 | 1 | Group II Intron IL |
| 271 | IL_30067.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|