Motif Atlas Releases 1.11 and 1.12
Changes in PDB files used for clustering
Release 1.11 has 214 PDB files, release 1.12 has 218 PDB files, 214 of them are identical.
No equivalence class representatives have been replaced.
4 new structures in release 1.12: 4C4W, 4J39, 4J5V, 4OO8.
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
Loading the Sankey diagram...
Changes in motif groups
Release 1.11 has 275 motif groups, release 1.12 has 276 motif groups, 253 of them are identical.
11 motif groups were updated, 11 groups are present only in release 1.11, 12 groups are only in release 1.12.
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_97217.10 | 248 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_41766.6 | 54 | Tandem cWW pairs (Not AU or GC) |
| 3 | IL_39199.4 | 53 | Hoogsteen-edge Platform, Single bulged base |
| 4 | IL_56465.4 | 47 | Single, unpaired intercalated base, consensus A |
| 5 | IL_44540.4 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 6 | IL_87904.5 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 7 | IL_82444.1 | 29 | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
| 8 | IL_13959.4 | 26 | Double Sheared (tSH-tHS) |
| 9 | IL_28947.2 | 22 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 10 | IL_73276.5 | 22 | C-loop |
| 11 | IL_93424.4 | 21 | tSH-inserted-tHW |
| 12 | IL_55938.4 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 13 | IL_92027.3 | 17 | 16S h21 S8 binding site |
| 14 | IL_24982.5 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 15 | IL_94430.5 | 16 | 16S h32-h33-h34 3WJ |
| 16 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 17 | IL_49493.4 | 13 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 18 | IL_31555.5 | 13 | Tandem sheared with inserted, unpaired purine. |
| 19 | IL_46648.6 | 13 | 23S H91 IL | Single-Base Intercalation Site |
| 20 | IL_43124.2 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 21 | IL_24546.4 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 22 | IL_58291.4 | 10 | Recurrent Sub-motif found in junctions |
| 23 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 24 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 25 | IL_02809.3 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 26 | IL_90459.3 | 9 | cWW AG or UU |
| 27 | IL_73000.2 | 7 | cHS-cWS |
| 28 | IL_46301.1 | 7 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 29 | IL_92321.4 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 30 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 31 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 32 | IL_25380.1 | 6 | LSU Helix 89 (H89) IL2 |
| 33 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 34 | IL_70173.1 | 6 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 35 | IL_70237.3 | 6 | |
| 36 | IL_97057.3 | 6 | |
| 37 | IL_08926.3 | 6 | 23S H91 IL |
| 38 | IL_77263.2 | 6 | Kink-turn from U4 |
| 39 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 40 | IL_90133.3 | 6 | |
| 41 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 42 | IL_02359.3 | 5 | |
| 43 | IL_05684.1 | 5 | tHS tHH bulge with S-turn | Double S-turn motif |
| 44 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 45 | IL_79083.3 | 5 | |
| 46 | IL_44067.4 | 5 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 47 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 48 | IL_98591.3 | 4 | |
| 49 | IL_39526.4 | 4 | |
| 50 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 51 | IL_39980.1 | 4 | |
| 52 | IL_82188.2 | 4 | LSU H68 IL from H.m. |
| 53 | IL_97296.1 | 4 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 54 | IL_95652.3 | 4 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 55 | IL_31663.1 | 4 | 23S H73 ILa : Part of larger Motif |
| 56 | IL_28572.2 | 4 | 16S h18 kink-turn like motif |
| 57 | IL_31066.3 | 4 | SSU Helix 44 (h44) extension |
| 58 | IL_38807.3 | 4 | |
| 59 | IL_45262.4 | 4 | |
| 60 | IL_54966.1 | 4 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 61 | IL_94403.5 | 4 | LSU H77 |
| 62 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 63 | IL_01080.1 | 4 | |
| 64 | IL_42251.1 | 4 | |
| 65 | IL_47758.2 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 66 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 67 | IL_09530.1 | 4 | Double S-turn motif |
| 68 | IL_48918.3 | 4 | Kink-turn variant |
| 69 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 70 | IL_25271.2 | 3 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 71 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 72 | IL_16415.2 | 3 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 73 | IL_16166.4 | 3 | 23S H91 IL |
| 74 | IL_05723.1 | 3 | |
| 75 | IL_62499.7 | 3 | |
| 76 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 77 | IL_35043.1 | 3 | cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base |
| 78 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 79 | IL_58586.2 | 3 | |
| 80 | IL_43946.1 | 3 | |
| 81 | IL_28003.1 | 3 | |
| 82 | IL_06180.1 | 3 | tHS tHH bulge with S-turn |
| 83 | IL_52173.1 | 3 | |
| 84 | IL_30840.2 | 3 | |
| 85 | IL_98421.4 | 3 | SSU Helix 12 (h12) IL |
| 86 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 87 | IL_89028.6 | 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. |
| 88 | IL_07300.2 | 3 | |
| 89 | IL_87065.1 | 3 | 23S H91 IL | Single-Base Intercalation Site |
| 90 | IL_34628.2 | 3 | Kink-turn |
| 91 | IL_50521.1 | 2 | |
| 92 | IL_09882.1 | 2 | |
| 93 | IL_46435.1 | 2 | |
| 94 | IL_09587.1 | 2 | |
| 95 | IL_16330.1 | 2 | |
| 96 | IL_87507.1 | 2 | tHS tHH bulge with S-turn |
| 97 | IL_70401.1 | 2 | |
| 98 | IL_87548.1 | 2 | |
| 99 | IL_52940.1 | 2 | |
| 100 | IL_80093.1 | 2 | |
| 101 | IL_21495.1 | 2 | |
| 102 | IL_40892.1 | 2 | |
| 103 | IL_33964.1 | 2 | |
| 104 | IL_33842.1 | 2 | |
| 105 | IL_11751.1 | 2 | |
| 106 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 107 | IL_97833.1 | 2 | |
| 108 | IL_12211.1 | 2 | |
| 109 | IL_37406.1 | 2 | |
| 110 | IL_97509.1 | 2 | Double sheared with wobble cWW. |
| 111 | IL_90735.1 | 2 | |
| 112 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 113 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 114 | IL_43877.1 | 2 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 115 | IL_39355.1 | 2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
| 116 | IL_69106.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 117 | IL_23262.4 | 2 | |
| 118 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 119 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 120 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 121 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 122 | IL_23414.1 | 2 | |
| 123 | IL_77076.1 | 2 | |
| 124 | IL_98566.1 | 2 | |
| 125 | IL_30381.1 | 2 | tHS tHH bulge with S-turn |
| 126 | IL_21639.1 | 2 | |
| 127 | IL_37197.1 | 2 | |
| 128 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 129 | IL_90057.1 | 2 | |
| 130 | IL_00998.1 | 2 | |
| 131 | IL_67887.1 | 2 | |
| 132 | IL_45794.1 | 2 | |
| 133 | IL_96446.1 | 2 | |
| 134 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 135 | IL_02835.1 | 1 | |
| 136 | IL_06421.1 | 1 | Single sheared with bulged bases |
| 137 | IL_20775.1 | 1 | tSH-inserted |
| 138 | IL_03741.1 | 1 | |
| 139 | IL_83856.1 | 1 | |
| 140 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 141 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 142 | IL_64589.1 | 1 | |
| 143 | IL_54470.1 | 1 | tHS tHH bulge with S-turn |
| 144 | IL_91044.1 | 1 | |
| 145 | IL_27668.1 | 1 | |
| 146 | IL_43316.1 | 1 | |
| 147 | IL_12507.1 | 1 | |
| 148 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 149 | IL_52958.1 | 1 | |
| 150 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 151 | IL_77014.1 | 1 | |
| 152 | IL_91078.1 | 1 | |
| 153 | IL_81398.1 | 1 | |
| 154 | IL_97842.1 | 1 | |
| 155 | IL_46306.1 | 1 | |
| 156 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 157 | IL_91089.1 | 1 | |
| 158 | IL_06847.1 | 1 | Group II Intron IL |
| 159 | IL_30067.1 | 1 | |
| 160 | IL_63952.1 | 1 | |
| 161 | IL_88865.1 | 1 | |
| 162 | IL_03110.1 | 1 | |
| 163 | IL_41791.1 | 1 | |
| 164 | IL_02897.1 | 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. |
| 165 | IL_80505.1 | 1 | |
| 166 | IL_69799.1 | 1 | |
| 167 | IL_47687.1 | 1 | |
| 168 | IL_80652.1 | 1 | |
| 169 | IL_54450.1 | 1 | |
| 170 | IL_71942.1 | 1 | |
| 171 | IL_37347.1 | 1 | |
| 172 | IL_06471.1 | 1 | |
| 173 | IL_68767.1 | 1 | |
| 174 | IL_17603.1 | 1 | |
| 175 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 176 | IL_99397.1 | 1 | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 177 | IL_60649.1 | 1 | Kink-turn |
| 178 | IL_52610.1 | 1 | |
| 179 | IL_05513.1 | 1 | |
| 180 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 181 | IL_06177.1 | 1 | cWW AG or UU |
| 182 | IL_82650.1 | 1 | |
| 183 | IL_22909.1 | 1 | |
| 184 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 185 | IL_55649.1 | 1 | |
| 186 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 187 | IL_75328.1 | 1 | |
| 188 | IL_31224.1 | 1 | 23S H91 IL |
| 189 | IL_05221.1 | 1 | |
| 190 | IL_26971.1 | 1 | |
| 191 | IL_56513.1 | 1 | |
| 192 | IL_15205.1 | 1 | |
| 193 | IL_87523.1 | 1 | |
| 194 | IL_77296.1 | 1 | |
| 195 | IL_87394.1 | 1 | |
| 196 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 197 | IL_40845.1 | 1 | |
| 198 | IL_39324.1 | 1 | |
| 199 | IL_86059.1 | 1 | |
| 200 | IL_25307.1 | 1 | |
| 201 | IL_26868.1 | 1 | |
| 202 | IL_25082.1 | 1 | |
| 203 | IL_53323.1 | 1 | |
| 204 | IL_59529.1 | 1 | |
| 205 | IL_91904.1 | 1 | |
| 206 | IL_21421.1 | 1 | |
| 207 | IL_85510.1 | 1 | |
| 208 | IL_21077.1 | 1 | |
| 209 | IL_03282.1 | 1 | |
| 210 | IL_42891.1 | 1 | |
| 211 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 212 | IL_57977.1 | 1 | |
| 213 | IL_76263.1 | 1 | |
| 214 | IL_91379.1 | 1 | |
| 215 | IL_11302.1 | 1 | |
| 216 | IL_89794.1 | 1 | |
| 217 | IL_28644.1 | 1 | |
| 218 | IL_52509.1 | 1 | |
| 219 | IL_27243.1 | 1 | |
| 220 | IL_88119.1 | 1 | |
| 221 | IL_98924.1 | 1 | |
| 222 | IL_25181.1 | 1 | |
| 223 | IL_09491.1 | 1 | |
| 224 | IL_58454.1 | 1 | |
| 225 | IL_88367.1 | 1 | |
| 226 | IL_49527.1 | 1 | |
| 227 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 228 | IL_47732.1 | 1 | |
| 229 | IL_50911.1 | 1 | 16S h34 ILa : Part of larger motif |
| 230 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 231 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 232 | IL_53988.1 | 1 | |
| 233 | IL_61730.1 | 1 | |
| 234 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 235 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 236 | IL_02957.1 | 1 | |
| 237 | IL_18675.1 | 1 | cWW-bulge-cWW |
| 238 | IL_40527.1 | 1 | Kink-turn |
| 239 | IL_49976.1 | 1 | |
| 240 | IL_57285.1 | 1 | |
| 241 | IL_46721.1 | 1 | |
| 242 | IL_85805.1 | 1 | |
| 243 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 244 | IL_83920.1 | 1 | |
| 245 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 246 | IL_11778.1 | 1 | |
| 247 | IL_06306.1 | 1 | |
| 248 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 249 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 250 | IL_57364.1 | 1 | LSU Helix 89 (H89) IL2 |
| 251 | IL_41139.1 | 1 | |
| 252 | IL_23448.1 | 1 | |
| 253 | IL_41153.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_47174.10 | 214 | cWW AG or water inserted cWW Y-Y. |
| 2 | IL_65553.8 | 23 | Kink-turn |
| 3 | IL_92109.3 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 4 | IL_17212.2 | 11 | cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
| 5 | IL_37104.3 | 11 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 6 | IL_25300.3 | 7 | 16S h19 IL and 23S H41 IL |
| 7 | IL_80348.3 | 3 | 23S H91 IL |
| 8 | IL_06211.3 | 3 | |
| 9 | IL_95150.6 | 3 | |
| 10 | IL_96206.3 | 2 | |
| 11 | IL_46034.3 | 2 |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_47475.1 | 2 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_74214.1 | 2 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 3 | IL_85015.1 | 2 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 4 | IL_22358.1 | 2 | |
| 5 | IL_95884.1 | 2 | |
| 6 | IL_31473.1 | 2 | |
| 7 | IL_91956.1 | 1 | |
| 8 | IL_27503.1 | 1 | |
| 9 | IL_30354.1 | 1 | |
| 10 | IL_95980.1 | 1 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 11 | IL_34076.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_47875.1 | 3 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_46990.1 | 2 | |
| 3 | IL_12024.1 | 2 | |
| 4 | IL_21644.1 | 2 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 5 | IL_24293.1 | 2 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 6 | IL_31039.1 | 2 | |
| 7 | IL_63253.1 | 1 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 8 | IL_70299.1 | 1 | |
| 9 | IL_13777.1 | 1 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 10 | IL_78513.1 | 1 | |
| 11 | IL_80714.1 | 1 | |
| 12 | IL_86336.1 | 1 |