Motif Atlas Releases 1.2 and 1.3
Changes in PDB files used for clustering
Release 1.2 has 200 PDB files, release 1.3 has 200 PDB files, 200 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_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 19 | IL_92109.1 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 20 | IL_94430.4 | 15 | 16S h32-h33-h34 3WJ |
| 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_46648.2 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 25 | IL_21304.2 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 26 | IL_24546.3 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 27 | IL_58291.3 | 9 | Recurrent Sub-motif found in junctions |
| 28 | IL_02809.2 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 29 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 30 | IL_90459.3 | 9 | cWW AG or UU |
| 31 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 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_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 36 | IL_70237.3 | 6 | |
| 37 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 38 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 39 | IL_97057.3 | 6 | |
| 40 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 41 | IL_44067.3 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 42 | IL_90133.2 | 6 | |
| 43 | IL_54420.1 | 6 | |
| 44 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 45 | IL_02359.3 | 5 | |
| 46 | IL_77263.1 | 5 | Kink-turn from U4 |
| 47 | IL_92484.1 | 5 | |
| 48 | IL_78732.3 | 5 | Double S-turn motif |
| 49 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 50 | IL_16207.1 | 5 | Single sheared with bulged bases |
| 51 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 52 | IL_08926.2 | 5 | 23S H91 IL |
| 53 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 54 | IL_45262.3 | 5 | |
| 55 | IL_79083.3 | 5 | |
| 56 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 57 | IL_42251.1 | 4 | |
| 58 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 59 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 60 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 61 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 62 | IL_16166.3 | 4 | 23S H91 IL |
| 63 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 64 | IL_38807.3 | 4 | |
| 65 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 66 | IL_98591.3 | 4 | |
| 67 | IL_08559.1 | 4 | LSU Helix 89 (H89) IL2 |
| 68 | IL_94403.1 | 4 | LSU H77 |
| 69 | IL_39526.4 | 4 | |
| 70 | IL_01080.1 | 4 | |
| 71 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 72 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 73 | IL_95150.3 | 3 | |
| 74 | IL_09520.2 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 75 | IL_30840.1 | 3 | |
| 76 | IL_34156.6 | 3 | cWW AG or UU |
| 77 | IL_48918.2 | 3 | Kink-turn variant |
| 78 | IL_62499.6 | 3 | |
| 79 | IL_80348.1 | 3 | 23S H91 IL |
| 80 | 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. |
| 81 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 82 | IL_98421.3 | 3 | SSU Helix 12 (h12) IL |
| 83 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 84 | IL_34628.2 | 3 | Kink-turn |
| 85 | IL_43946.1 | 3 | |
| 86 | IL_58586.2 | 3 | |
| 87 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 88 | IL_05723.1 | 3 | |
| 89 | IL_56077.1 | 3 | |
| 90 | IL_10647.1 | 3 | tHS tHH bulge with S-turn |
| 91 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 92 | IL_52173.1 | 3 | |
| 93 | IL_71565.3 | 3 | |
| 94 | IL_75447.1 | 3 | |
| 95 | IL_92267.1 | 3 | 23S H73 ILa : Part of larger Motif |
| 96 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 97 | IL_33964.1 | 2 | |
| 98 | IL_37406.1 | 2 | |
| 99 | IL_52940.1 | 2 | |
| 100 | IL_77076.1 | 2 | |
| 101 | IL_80093.1 | 2 | |
| 102 | IL_12211.1 | 2 | |
| 103 | IL_21495.1 | 2 | |
| 104 | IL_27892.1 | 2 | |
| 105 | IL_46435.1 | 2 | |
| 106 | IL_55287.1 | 2 | |
| 107 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 108 | IL_91273.1 | 2 | |
| 109 | IL_09587.1 | 2 | |
| 110 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 111 | IL_19898.1 | 2 | |
| 112 | IL_98566.1 | 2 | |
| 113 | IL_07300.1 | 2 | |
| 114 | IL_09882.1 | 2 | |
| 115 | IL_23262.4 | 2 | |
| 116 | IL_40892.1 | 2 | |
| 117 | IL_49550.1 | 2 | tHS tHH bulge with S-turn |
| 118 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 119 | IL_90057.1 | 2 | |
| 120 | IL_09901.1 | 2 | tHS tHH bulge with S-turn |
| 121 | IL_23414.1 | 2 | |
| 122 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 123 | IL_50521.1 | 2 | |
| 124 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 125 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 126 | IL_00998.1 | 2 | |
| 127 | IL_16252.3 | 2 | 23S H91 IL |
| 128 | IL_28942.1 | 2 | |
| 129 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 130 | IL_87548.1 | 2 | |
| 131 | IL_01054.1 | 2 | |
| 132 | IL_16330.1 | 2 | |
| 133 | IL_24358.1 | 2 | |
| 134 | IL_37197.1 | 2 | |
| 135 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 136 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 137 | IL_09348.5 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 138 | IL_11751.1 | 2 | |
| 139 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 140 | IL_33925.1 | 2 | |
| 141 | IL_45794.1 | 2 | |
| 142 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 143 | IL_88180.1 | 2 | cWW-bulge-cWW |
| 144 | IL_97833.1 | 2 | |
| 145 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 146 | IL_06471.1 | 1 | |
| 147 | IL_09491.1 | 1 | |
| 148 | IL_11778.1 | 1 | |
| 149 | IL_15205.1 | 1 | |
| 150 | IL_17603.1 | 1 | |
| 151 | IL_21421.1 | 1 | |
| 152 | IL_26971.1 | 1 | |
| 153 | IL_30354.1 | 1 | |
| 154 | IL_46306.1 | 1 | |
| 155 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 156 | IL_57977.1 | 1 | |
| 157 | IL_61730.1 | 1 | |
| 158 | IL_67735.1 | 1 | |
| 159 | IL_88367.1 | 1 | |
| 160 | IL_91089.1 | 1 | |
| 161 | IL_97842.1 | 1 | |
| 162 | IL_02690.1 | 1 | |
| 163 | IL_04550.1 | 1 | tHS tHH bulge with S-turn |
| 164 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 165 | 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. |
| 166 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 167 | IL_25082.1 | 1 | |
| 168 | IL_37715.1 | 1 | |
| 169 | IL_40527.1 | 1 | Kink-turn |
| 170 | IL_52958.1 | 1 | |
| 171 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 172 | IL_85805.1 | 1 | |
| 173 | IL_05221.1 | 1 | |
| 174 | IL_06847.1 | 1 | Group II Intron IL |
| 175 | IL_12486.1 | 1 | |
| 176 | IL_25181.1 | 1 | |
| 177 | IL_28468.1 | 1 | Single sheared with bulged bases |
| 178 | IL_37990.1 | 1 | |
| 179 | IL_40845.1 | 1 | |
| 180 | IL_43316.1 | 1 | |
| 181 | IL_53323.1 | 1 | |
| 182 | IL_55649.1 | 1 | |
| 183 | IL_58454.1 | 1 | |
| 184 | IL_63952.1 | 1 | |
| 185 | IL_77296.1 | 1 | |
| 186 | IL_82650.1 | 1 | |
| 187 | IL_86059.1 | 1 | |
| 188 | IL_89794.1 | 1 | |
| 189 | IL_91904.1 | 1 | |
| 190 | IL_95774.1 | 1 | tHS tHH bulge with S-turn |
| 191 | IL_02835.1 | 1 | |
| 192 | IL_05462.1 | 1 | |
| 193 | IL_12507.1 | 1 | |
| 194 | IL_20775.1 | 1 | tSH-inserted |
| 195 | IL_31290.1 | 1 | |
| 196 | IL_46721.1 | 1 | |
| 197 | IL_64589.1 | 1 | |
| 198 | IL_80505.1 | 1 | |
| 199 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 200 | IL_02957.1 | 1 | |
| 201 | IL_21221.1 | 1 | SSU Helix 12 (h12) IL |
| 202 | IL_28644.1 | 1 | |
| 203 | IL_34868.1 | 1 | LSU Eukaryal Helix 96 (H96) IL1 |
| 204 | IL_41139.1 | 1 | |
| 205 | IL_53988.1 | 1 | |
| 206 | IL_59529.1 | 1 | |
| 207 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 208 | IL_80652.1 | 1 | |
| 209 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 210 | IL_97073.1 | 1 | |
| 211 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 212 | IL_03110.1 | 1 | |
| 213 | IL_06306.1 | 1 | |
| 214 | IL_13434.1 | 1 | |
| 215 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 216 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 217 | IL_39324.1 | 1 | |
| 218 | IL_41341.1 | 1 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 219 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 220 | IL_78809.1 | 1 | |
| 221 | IL_81398.1 | 1 | |
| 222 | IL_83856.1 | 1 | |
| 223 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 224 | IL_98924.1 | 1 | |
| 225 | IL_03282.1 | 1 | |
| 226 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 227 | IL_11302.1 | 1 | |
| 228 | IL_13682.1 | 1 | |
| 229 | IL_25307.1 | 1 | |
| 230 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 231 | IL_47687.1 | 1 | |
| 232 | IL_52509.1 | 1 | |
| 233 | IL_54450.1 | 1 | |
| 234 | IL_56513.1 | 1 | |
| 235 | IL_60643.1 | 1 | |
| 236 | IL_65788.1 | 1 | |
| 237 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 238 | IL_82113.1 | 1 | |
| 239 | IL_83920.1 | 1 | |
| 240 | IL_91044.1 | 1 | |
| 241 | IL_03741.1 | 1 | |
| 242 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 243 | IL_26868.1 | 1 | |
| 244 | IL_30067.1 | 1 | |
| 245 | IL_37347.1 | 1 | |
| 246 | IL_41791.1 | 1 | |
| 247 | IL_47732.1 | 1 | |
| 248 | IL_52610.1 | 1 | |
| 249 | IL_54576.1 | 1 | |
| 250 | IL_60649.1 | 1 | Kink-turn |
| 251 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 252 | IL_71942.1 | 1 | |
| 253 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 254 | IL_85510.1 | 1 | |
| 255 | IL_91078.1 | 1 | |
| 256 | IL_92280.1 | 1 | |
| 257 | 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 |
|---|