Motif Atlas Releases 0.7 and 0.8
Changes in PDB files used for clustering
Release 0.7 has 192 PDB files, release 0.8 has 192 PDB files, 192 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 0.7 has 263 motif groups, release 0.8 has 263 motif groups, 263 of them are identical.
0 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.
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_97217.2 | 234 | |
| 2 | IL_47174.2 | 200 | 16S h34 ILa : Part of larger motif |
| 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_87904.2 | 31 | Triple sheared |
| 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_65553.2 | 21 | 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_06429.1 | 16 | 16S h19 IL and 23S H41 IL | 1 or 2 bulged bases |
| 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_31555.2 | 15 | 16S decoding site |
| 20 | IL_94430.2 | 14 | 16S h32-h33-h34 3WJ |
| 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_92114.2 | 9 | GAAA loop receptor "platform" motif |
| 28 | IL_58291.2 | 9 | Recurrent Sub-motif found in junctions |
| 29 | IL_47444.2 | 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_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_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 37 | IL_08926.1 | 6 | 23S H91 IL |
| 38 | IL_97057.2 | 6 | |
| 39 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
| 40 | IL_70237.3 | 6 | |
| 41 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
| 42 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
| 43 | IL_24022.2 | 6 | |
| 44 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
| 45 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
| 46 | IL_10007.1 | 6 | Single sheared with bulged bases |
| 47 | IL_77263.1 | 5 | Kink-turn from U4 |
| 48 | IL_79083.2 | 5 | |
| 49 | IL_80179.2 | 5 | |
| 50 | IL_01239.1 | 5 | |
| 51 | IL_92484.1 | 5 | |
| 52 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 53 | IL_07911.1 | 5 | |
| 54 | IL_78732.3 | 5 | Double S-turn motif |
| 55 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 56 | IL_02359.2 | 5 | |
| 57 | IL_45262.2 | 5 | |
| 58 | IL_40387.2 | 5 | |
| 59 | IL_38807.2 | 4 | |
| 60 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 61 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 62 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 63 | IL_98591.2 | 4 | |
| 64 | IL_64184.2 | 4 | |
| 65 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 66 | IL_39526.2 | 4 | |
| 67 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 68 | IL_21333.1 | 4 | tSH-tHW-bulge |
| 69 | IL_98556.1 | 4 | |
| 70 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 71 | IL_43946.1 | 3 | |
| 72 | IL_09348.2 | 3 | |
| 73 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 74 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
| 75 | IL_23262.3 | 3 | |
| 76 | IL_52173.1 | 3 | |
| 77 | IL_75447.1 | 3 | |
| 78 | IL_45808.1 | 3 | |
| 79 | IL_98421.1 | 3 | |
| 80 | IL_58586.2 | 3 | |
| 81 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 82 | IL_16252.2 | 3 | 23S H91 IL |
| 83 | IL_15840.1 | 3 | |
| 84 | IL_71565.1 | 3 | |
| 85 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 86 | IL_95150.2 | 3 | |
| 87 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 88 | IL_89028.1 | 3 | Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 89 | IL_30840.1 | 3 | |
| 90 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 91 | IL_34628.2 | 3 | Kink-turn |
| 92 | IL_62499.2 | 3 | |
| 93 | IL_34156.2 | 3 | cWW AG or UU |
| 94 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 95 | IL_97833.1 | 2 | |
| 96 | IL_16166.1 | 2 | |
| 97 | IL_74291.1 | 2 | |
| 98 | IL_01054.1 | 2 | |
| 99 | IL_37406.1 | 2 | |
| 100 | IL_12068.1 | 2 | |
| 101 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 102 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 103 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 104 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 105 | IL_98566.1 | 2 | |
| 106 | IL_87173.1 | 2 | |
| 107 | IL_25174.1 | 2 | |
| 108 | IL_81441.1 | 2 | |
| 109 | IL_92459.1 | 2 | |
| 110 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 111 | IL_55287.1 | 2 | |
| 112 | IL_37197.1 | 2 | |
| 113 | IL_99575.1 | 2 | |
| 114 | IL_48285.1 | 2 | Leadzyme Motif |
| 115 | IL_80093.1 | 2 | |
| 116 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
| 117 | IL_00998.1 | 2 | |
| 118 | IL_45794.1 | 2 | |
| 119 | IL_50521.1 | 2 | |
| 120 | IL_09882.1 | 2 | |
| 121 | IL_12269.1 | 2 | |
| 122 | IL_46435.1 | 2 | |
| 123 | IL_23414.1 | 2 | |
| 124 | IL_43933.1 | 2 | |
| 125 | IL_91026.1 | 2 | |
| 126 | IL_87548.1 | 2 | |
| 127 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 128 | IL_52940.1 | 2 | |
| 129 | IL_90057.1 | 2 | |
| 130 | IL_12211.1 | 2 | |
| 131 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 132 | IL_21495.1 | 2 | |
| 133 | IL_28942.1 | 2 | |
| 134 | IL_16330.1 | 2 | |
| 135 | IL_40892.1 | 2 | |
| 136 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 137 | IL_78674.1 | 2 | tHS tHH bulge with S-turn |
| 138 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 139 | IL_74876.1 | 2 | |
| 140 | IL_14023.1 | 2 | |
| 141 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 142 | IL_82650.1 | 1 | |
| 143 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 144 | IL_52509.1 | 1 | |
| 145 | IL_12486.1 | 1 | |
| 146 | IL_12233.1 | 1 | |
| 147 | IL_77014.1 | 1 | |
| 148 | IL_03741.1 | 1 | |
| 149 | IL_82113.1 | 1 | |
| 150 | IL_05221.1 | 1 | |
| 151 | IL_26971.1 | 1 | |
| 152 | IL_07375.1 | 1 | |
| 153 | IL_58454.1 | 1 | |
| 154 | IL_88367.1 | 1 | |
| 155 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 156 | IL_40845.1 | 1 | |
| 157 | IL_88865.1 | 1 | |
| 158 | IL_76263.1 | 1 | |
| 159 | IL_25307.1 | 1 | |
| 160 | IL_26868.1 | 1 | |
| 161 | IL_55649.1 | 1 | |
| 162 | IL_54450.1 | 1 | |
| 163 | IL_31241.1 | 1 | |
| 164 | IL_26241.1 | 1 | |
| 165 | IL_71942.1 | 1 | |
| 166 | IL_91078.1 | 1 | |
| 167 | IL_56779.1 | 1 | |
| 168 | IL_53323.1 | 1 | |
| 169 | IL_59529.1 | 1 | |
| 170 | IL_02957.1 | 1 | |
| 171 | IL_18755.1 | 1 | |
| 172 | IL_40527.1 | 1 | Kink-turn |
| 173 | IL_92280.1 | 1 | |
| 174 | IL_91379.1 | 1 | |
| 175 | IL_11302.1 | 1 | |
| 176 | IL_89794.1 | 1 | |
| 177 | IL_07675.1 | 1 | tHS tHH bulge with S-turn |
| 178 | IL_25739.1 | 1 | M-Box Riboswitch |
| 179 | IL_37715.1 | 1 | |
| 180 | IL_22579.1 | 1 | |
| 181 | IL_41849.1 | 1 | |
| 182 | IL_75328.1 | 1 | |
| 183 | IL_95939.1 | 1 | |
| 184 | IL_25082.1 | 1 | |
| 185 | IL_98924.1 | 1 | |
| 186 | IL_25181.1 | 1 | |
| 187 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 188 | IL_41139.1 | 1 | |
| 189 | IL_02835.1 | 1 | |
| 190 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 191 | IL_22858.1 | 1 | |
| 192 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 193 | IL_53988.1 | 1 | |
| 194 | IL_20775.1 | 1 | tSH-inserted |
| 195 | IL_61730.1 | 1 | |
| 196 | IL_53423.1 | 1 | |
| 197 | IL_24143.1 | 1 | Yeast 18S |
| 198 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 199 | IL_90880.1 | 1 | |
| 200 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 201 | IL_96260.1 | 1 | |
| 202 | IL_85805.1 | 1 | |
| 203 | IL_03110.1 | 1 | |
| 204 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 205 | IL_05462.1 | 1 | |
| 206 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 207 | IL_65788.1 | 1 | |
| 208 | IL_55934.1 | 1 | kink-turn-like |
| 209 | IL_27243.1 | 1 | |
| 210 | IL_78809.1 | 1 | |
| 211 | IL_13682.1 | 1 | |
| 212 | IL_67735.1 | 1 | |
| 213 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 214 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 215 | IL_17603.1 | 1 | |
| 216 | IL_15205.1 | 1 | |
| 217 | IL_91089.1 | 1 | |
| 218 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 219 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 220 | IL_43316.1 | 1 | |
| 221 | IL_83920.1 | 1 | |
| 222 | IL_88403.1 | 1 | |
| 223 | IL_80652.1 | 1 | |
| 224 | IL_32080.1 | 1 | |
| 225 | IL_61723.1 | 1 | |
| 226 | IL_54576.1 | 1 | |
| 227 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 228 | IL_37990.1 | 1 | |
| 229 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 230 | IL_47457.1 | 1 | |
| 231 | IL_23448.1 | 1 | |
| 232 | IL_57977.1 | 1 | |
| 233 | IL_39324.1 | 1 | |
| 234 | IL_41791.1 | 1 | |
| 235 | IL_86059.1 | 1 | |
| 236 | IL_12507.1 | 1 | |
| 237 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 238 | IL_52958.1 | 1 | |
| 239 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 240 | IL_97073.1 | 1 | |
| 241 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 242 | IL_29949.1 | 1 | |
| 243 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 244 | IL_06306.1 | 1 | |
| 245 | IL_97842.1 | 1 | |
| 246 | IL_56513.1 | 1 | |
| 247 | IL_30390.1 | 1 | |
| 248 | IL_60643.1 | 1 | |
| 249 | IL_63952.1 | 1 | |
| 250 | IL_52752.1 | 1 | |
| 251 | IL_13942.1 | 1 | |
| 252 | IL_80505.1 | 1 | |
| 253 | IL_47687.1 | 1 | |
| 254 | IL_62352.1 | 1 | |
| 255 | IL_02690.1 | 1 | |
| 256 | IL_11869.1 | 1 | |
| 257 | IL_41009.1 | 1 | |
| 258 | IL_81398.1 | 1 | |
| 259 | IL_37347.1 | 1 | |
| 260 | IL_46306.1 | 1 | |
| 261 | IL_91904.1 | 1 | |
| 262 | IL_21421.1 | 1 | |
| 263 | IL_85510.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|