Changes in PDB files used for clustering

Release 0.11 has 196 PDB files, release 0.12 has 196 PDB files, 196 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

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Changes in motif groups

Release 0.11 has 266 motif groups, release 0.12 has 266 motif groups, 266 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.11, 0 groups are only in release 0.12.

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 idInstancesDescription
1IL_97217.42351-3 bulged nucleotides, same chain
2IL_47174.5203cWW AG or water inserted cWW Y-Y.
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.331Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_65553.422Kink-turn
12IL_32390.22116S h19 IL and 23S H41 IL
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_85647.216Sarcin-ricin parent motif with 15 Nts
17IL_06429.216cWW-bulge-cWW
18IL_94430.31516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_46648.11123S H91 IL | Single-Base Intercalation Site
23IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_40090.21116S h34 ILa : Part of larger motif
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.39SRP Loop E-like motif
28IL_92114.39GAAA loop receptor "platform" motif
29IL_58291.29Recurrent Sub-motif found in junctions
30IL_90459.28cWW AG or UU
31IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_86357.27LSU Helix 61 IL2
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_73000.27cHS-cWS
36IL_70237.36
37IL_97057.26
38IL_54420.16
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_24022.26
41IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
42IL_10007.16Single sheared with bulged bases
43IL_08926.1623S H91 IL
44IL_53635.26LSU Helix 32 (H32) IL
45IL_72158.26LSU Helix 62 (H62) IL
46IL_89088.1616S h19 IL and 23S H41 IL
47IL_25230.26Bacterial 5S rRNA Loop E
48IL_82188.15LSU H68 IL from H.m.
49IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
50IL_77263.15Kink-turn from U4
51IL_90133.15
52IL_01239.15
53IL_02359.25
54IL_45262.25
55IL_78732.35Double S-turn motif
56IL_79083.25
57IL_92484.15
58IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
59IL_98556.34
60IL_31066.24SSU Helix 44 (h44) extension
61IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62IL_10005.14
63IL_21333.14tSH-tHW-bulge
64IL_38807.24
65IL_98591.24
66IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
67IL_39526.34
68IL_22732.14tSH-inserted-tHS
69IL_28572.1416S h18 kink-turn like motif
70IL_40387.44LSU Helix 89 (H89) IL2
71IL_34363.13Kink-turn from 23S H42
72IL_52173.13
73IL_58586.23
74IL_79955.23SSU Helix (23) h23 IL1
75IL_34628.23Kink-turn
76IL_43946.13
77IL_82563.13Thi-box riboswitch T-loop
78IL_91547.13tHS tHH bulge with S-turn
79IL_36254.13
80IL_80494.23LSU H58 IL2 H.m.
81IL_37053.13Kink-turn from 23S H58
82IL_71565.13
83IL_75447.13
84IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
85IL_95150.33
86IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
87IL_16166.23
88IL_23262.33
89IL_53774.13Single sheared with bulged bases
90IL_62499.43
91IL_98421.23SSU Helix 12 (h12) IL
92IL_09348.33cWW-L-cWW-cWW
93IL_16252.2323S H91 IL
94IL_30840.13
95IL_34156.43cWW AG or UU
96IL_77076.12
97IL_91132.12
98IL_00998.12
99IL_09882.12
100IL_16330.12
101IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
102IL_58811.12
103IL_70280.12Double sheared with wobble cWW.
104IL_74876.12
105IL_80093.12
106IL_87548.12
107IL_90057.12
108IL_98566.12
109IL_01054.12
110IL_16377.12
111IL_40892.12
112IL_52940.12
113IL_65137.12Kink-turn like motif in Group I Intron
114IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
115IL_94744.12Sarcin-ricin motif with extra cWW GA pair
116IL_21495.12
117IL_31707.12Vitamin B12 aptamer
118IL_41397.22LSU Helix 96 (H96) IL2
119IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
120IL_82831.22Kink-turn from 16S H23
121IL_97833.12
122IL_07300.12
123IL_11751.12
124IL_37197.12
125IL_45794.12
126IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
127IL_76095.32Motif from Hairpin Ribozyme
128IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
129IL_15840.22Triple Sheared with unpaired, inserted A
130IL_25174.12
131IL_55287.12
132IL_81441.12
133IL_12211.12
134IL_28942.12
135IL_33965.12tHS tHH bulge with S-turn
136IL_37406.12
137IL_46435.12
138IL_50521.12
139IL_69901.12
140IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
141IL_89231.12LSU H77
142IL_23414.12
143IL_37715.11
144IL_40527.11Kink-turn
145IL_43316.11
146IL_53988.11
147IL_55934.11kink-turn-like
148IL_83920.11
149IL_87544.11
150IL_89794.11
151IL_03110.11
152IL_06468.1116S h40 3WJ E.c.
153IL_12507.11
154IL_23639.11tWH-tHS-L-cWW
155IL_37990.11
156IL_40845.11
157IL_52509.11
158IL_63952.11
159IL_77195.11
160IL_85510.11
161IL_97073.11
162IL_03282.11
163IL_06471.11
164IL_25307.11
165IL_31241.11
166IL_54450.11
167IL_59529.11
168IL_75415.11Pseudo-knot forming internal loop
169IL_82601.11Tandem cWW water-inserted CU pairs
170IL_91904.11
171IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
172IL_03741.11
173IL_06808.11Double sheared (tSH-tSH) one bulged base.
174IL_13682.11
175IL_21421.11
176IL_26868.11
177IL_41139.11
178IL_47687.11
179IL_52958.11
180IL_54576.11
181IL_56513.11
182IL_60643.11
183IL_77296.11
184IL_80505.11
185IL_82650.11
186IL_85805.11
187IL_88367.11
188IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
189IL_05221.11
190IL_06847.11Group II Intron IL
191IL_11302.11
192IL_17603.11
193IL_26971.11
194IL_37150.11tHS tHH bulge with S-turn
195IL_39324.11
196IL_53323.11
197IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
198IL_60649.11Kink-turn
199IL_65788.11
200IL_71685.11Sarcin-like with an intercalated basepair
201IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
202IL_80652.11
203IL_86059.11
204IL_88403.11
205IL_90880.11
206IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
207IL_98688.11
208IL_02690.11
209IL_05462.11
210IL_15205.11
211IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
212IL_22579.11
213IL_25082.11
214IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
215IL_47968.11
216IL_53423.11
217IL_57977.11
218IL_61730.11
219IL_66744.11SSU Helix 21 (h21) IL2 E.coli
220IL_71942.11
221IL_81398.11
222IL_83250.1116S h40 3WJ T.th.
223IL_91044.11
224IL_92280.11
225IL_97842.11
226IL_98924.11
227IL_06306.11
228IL_11869.11
229IL_18755.11
230IL_37347.11
231IL_41791.11
232IL_46306.11
233IL_61991.11
234IL_67735.11
235IL_76256.11
236IL_78809.11
237IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
238IL_91078.11
239IL_97961.11
240IL_02835.11
241IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
242IL_20775.11tSH-inserted
243IL_25181.11
244IL_41864.11Part of H71 junction in 23S rRNA from T.th.
245IL_55649.11
246IL_58454.11
247IL_76486.11Sarcin-ricin motif with syn G
248IL_82113.11
249IL_83856.11
250IL_91089.11
251IL_96031.11tHS tHH bulge with S-turn
252IL_02957.11
253IL_12486.11
254IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription
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