Motif Atlas Releases 0.7 and 0.8
Changes in PDB files used for clustering
Release 0.7 has 191 PDB files, release 0.8 has 191 PDB files, 191 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_32390.2 | 21 | 16S h19 IL and 23S H41 IL |
| 12 | IL_65553.2 | 21 | Kink-turn |
| 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_49493.2 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 21 | IL_94430.2 | 14 | 16S h32-h33-h34 3WJ |
| 22 | IL_46648.1 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 23 | IL_21304.1 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 24 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
| 25 | IL_40090.2 | 11 | 16S h34 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_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_02809.1 | 8 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 31 | IL_90459.2 | 8 | cWW AG or UU |
| 32 | IL_92321.2 | 8 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 33 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 34 | IL_73000.2 | 7 | cHS-cWS |
| 35 | IL_86357.2 | 7 | LSU Helix 61 IL2 |
| 36 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
| 37 | IL_10007.1 | 6 | Single sheared with bulged bases |
| 38 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
| 39 | IL_70237.3 | 6 | |
| 40 | IL_97057.2 | 6 | |
| 41 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
| 42 | IL_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 43 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
| 44 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
| 45 | IL_24022.2 | 6 | |
| 46 | IL_08926.1 | 6 | 23S H91 IL |
| 47 | IL_79083.2 | 5 | |
| 48 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 49 | IL_77263.1 | 5 | Kink-turn from U4 |
| 50 | IL_80179.2 | 5 | |
| 51 | IL_92484.1 | 5 | |
| 52 | IL_01239.1 | 5 | |
| 53 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 54 | IL_78732.3 | 5 | Double S-turn motif |
| 55 | IL_02359.2 | 5 | |
| 56 | IL_07911.1 | 5 | |
| 57 | IL_45262.2 | 5 | |
| 58 | IL_40387.2 | 5 | |
| 59 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 60 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 61 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 62 | IL_38807.2 | 4 | |
| 63 | IL_98556.1 | 4 | |
| 64 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 65 | IL_98591.2 | 4 | |
| 66 | IL_21333.1 | 4 | tSH-tHW-bulge |
| 67 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 68 | IL_39526.2 | 4 | |
| 69 | IL_64184.2 | 4 | |
| 70 | IL_95150.2 | 3 | |
| 71 | IL_45808.1 | 3 | |
| 72 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 73 | IL_09348.2 | 3 | |
| 74 | IL_30840.1 | 3 | |
| 75 | IL_34156.2 | 3 | cWW AG or UU |
| 76 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 77 | IL_98421.1 | 3 | |
| 78 | IL_15840.1 | 3 | |
| 79 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
| 80 | IL_62499.2 | 3 | |
| 81 | IL_23262.3 | 3 | |
| 82 | IL_34628.2 | 3 | Kink-turn |
| 83 | IL_43946.1 | 3 | |
| 84 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 85 | IL_16252.2 | 3 | 23S H91 IL |
| 86 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 87 | IL_52173.1 | 3 | |
| 88 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 89 | IL_58586.2 | 3 | |
| 90 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 91 | IL_89028.1 | 3 | Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 92 | IL_71565.1 | 3 | |
| 93 | IL_75447.1 | 3 | |
| 94 | IL_87173.1 | 2 | |
| 95 | IL_90057.1 | 2 | |
| 96 | IL_97833.1 | 2 | |
| 97 | IL_99575.1 | 2 | |
| 98 | IL_14023.1 | 2 | |
| 99 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 100 | IL_81441.1 | 2 | |
| 101 | IL_87548.1 | 2 | |
| 102 | IL_12269.1 | 2 | |
| 103 | IL_48285.1 | 2 | Leadzyme Motif |
| 104 | IL_55287.1 | 2 | |
| 105 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 106 | IL_09882.1 | 2 | |
| 107 | IL_40892.1 | 2 | |
| 108 | IL_43933.1 | 2 | |
| 109 | IL_46435.1 | 2 | |
| 110 | IL_80093.1 | 2 | |
| 111 | IL_91026.1 | 2 | |
| 112 | IL_92459.1 | 2 | |
| 113 | IL_00998.1 | 2 | |
| 114 | IL_16166.1 | 2 | |
| 115 | IL_25174.1 | 2 | |
| 116 | IL_50521.1 | 2 | |
| 117 | IL_98566.1 | 2 | |
| 118 | IL_01054.1 | 2 | |
| 119 | IL_23414.1 | 2 | |
| 120 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 121 | IL_74291.1 | 2 | |
| 122 | IL_78674.1 | 2 | tHS tHH bulge with S-turn |
| 123 | IL_16330.1 | 2 | |
| 124 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 125 | IL_37197.1 | 2 | |
| 126 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 127 | IL_74876.1 | 2 | |
| 128 | IL_12068.1 | 2 | |
| 129 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 130 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 131 | IL_28942.1 | 2 | |
| 132 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 133 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 134 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
| 135 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 136 | IL_12211.1 | 2 | |
| 137 | IL_21495.1 | 2 | |
| 138 | IL_37406.1 | 2 | |
| 139 | IL_45794.1 | 2 | |
| 140 | IL_52940.1 | 2 | |
| 141 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 142 | IL_12233.1 | 1 | |
| 143 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 144 | IL_22579.1 | 1 | |
| 145 | IL_25739.1 | 1 | M-Box Riboswitch |
| 146 | IL_30390.1 | 1 | |
| 147 | IL_37715.1 | 1 | |
| 148 | IL_40527.1 | 1 | Kink-turn |
| 149 | IL_41849.1 | 1 | |
| 150 | IL_52958.1 | 1 | |
| 151 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 152 | IL_61730.1 | 1 | |
| 153 | IL_65788.1 | 1 | |
| 154 | IL_71942.1 | 1 | |
| 155 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 156 | IL_83920.1 | 1 | |
| 157 | IL_92280.1 | 1 | |
| 158 | IL_97842.1 | 1 | |
| 159 | IL_02835.1 | 1 | |
| 160 | IL_15205.1 | 1 | |
| 161 | IL_18755.1 | 1 | |
| 162 | IL_26241.1 | 1 | |
| 163 | IL_37990.1 | 1 | |
| 164 | IL_40845.1 | 1 | |
| 165 | IL_43316.1 | 1 | |
| 166 | IL_46306.1 | 1 | |
| 167 | IL_53323.1 | 1 | |
| 168 | IL_57977.1 | 1 | |
| 169 | IL_62352.1 | 1 | |
| 170 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 171 | IL_82113.1 | 1 | |
| 172 | IL_85510.1 | 1 | |
| 173 | IL_90880.1 | 1 | |
| 174 | IL_95939.1 | 1 | |
| 175 | IL_02957.1 | 1 | |
| 176 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 177 | IL_12486.1 | 1 | |
| 178 | IL_20775.1 | 1 | tSH-inserted |
| 179 | IL_22858.1 | 1 | |
| 180 | IL_25082.1 | 1 | |
| 181 | IL_26868.1 | 1 | |
| 182 | IL_53423.1 | 1 | |
| 183 | IL_55649.1 | 1 | |
| 184 | IL_67735.1 | 1 | |
| 185 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 186 | IL_88367.1 | 1 | |
| 187 | IL_96260.1 | 1 | |
| 188 | IL_03110.1 | 1 | |
| 189 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 190 | IL_12507.1 | 1 | |
| 191 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 192 | IL_26971.1 | 1 | |
| 193 | IL_31241.1 | 1 | |
| 194 | IL_41009.1 | 1 | |
| 195 | IL_55934.1 | 1 | kink-turn-like |
| 196 | IL_58454.1 | 1 | |
| 197 | IL_85805.1 | 1 | |
| 198 | IL_88403.1 | 1 | |
| 199 | IL_91078.1 | 1 | |
| 200 | IL_03741.1 | 1 | |
| 201 | IL_07375.1 | 1 | |
| 202 | IL_11302.1 | 1 | |
| 203 | IL_25181.1 | 1 | |
| 204 | IL_39324.1 | 1 | |
| 205 | IL_41139.1 | 1 | |
| 206 | IL_63952.1 | 1 | |
| 207 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 208 | IL_86059.1 | 1 | |
| 209 | IL_91089.1 | 1 | |
| 210 | IL_97073.1 | 1 | |
| 211 | IL_05221.1 | 1 | |
| 212 | IL_07675.1 | 1 | tHS tHH bulge with S-turn |
| 213 | IL_11869.1 | 1 | |
| 214 | IL_13682.1 | 1 | |
| 215 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 216 | IL_52509.1 | 1 | |
| 217 | IL_53988.1 | 1 | |
| 218 | IL_59529.1 | 1 | |
| 219 | IL_80505.1 | 1 | |
| 220 | IL_82650.1 | 1 | |
| 221 | IL_91904.1 | 1 | |
| 222 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 223 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 224 | IL_05462.1 | 1 | |
| 225 | IL_13942.1 | 1 | |
| 226 | IL_21421.1 | 1 | |
| 227 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 228 | IL_37347.1 | 1 | |
| 229 | IL_47457.1 | 1 | |
| 230 | IL_52752.1 | 1 | |
| 231 | IL_54450.1 | 1 | |
| 232 | IL_56513.1 | 1 | |
| 233 | IL_60643.1 | 1 | |
| 234 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 235 | IL_80652.1 | 1 | |
| 236 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 237 | IL_89794.1 | 1 | |
| 238 | IL_98924.1 | 1 | |
| 239 | IL_02690.1 | 1 | |
| 240 | IL_06306.1 | 1 | |
| 241 | IL_17603.1 | 1 | |
| 242 | IL_24143.1 | 1 | Yeast 18S |
| 243 | IL_25307.1 | 1 | |
| 244 | IL_29949.1 | 1 | |
| 245 | IL_32080.1 | 1 | |
| 246 | IL_41791.1 | 1 | |
| 247 | IL_47687.1 | 1 | |
| 248 | IL_54576.1 | 1 | |
| 249 | IL_56779.1 | 1 | |
| 250 | IL_61723.1 | 1 | |
| 251 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 252 | IL_78809.1 | 1 | |
| 253 | IL_81398.1 | 1 | |
| 254 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
Updated motif groups
| # | Motif id | Instances | Description |
|---|
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|